1. Module 1: Science, Biology and Evolution
1. Studio Biology - What is it?
1. Studio Biology - What is it?
2. Science as a way of knowing
1. Science as a way of knowing
3. Evolution
1. Evolution
4. Taxonomy and phylogeny
2. Module 2: Ecology
1. Introduction to Ecology and Ecosystems
1. The Scope of Ecology
. Ecology of Ecosystems
. The Laws of Thermodynamics
. Energy Flow
. Biogeochemical Cycles
. Biogeography
Biomes
8. Aquatic Biomes
2. Population Ecology
1. Population
2. Population Growth
3. Population Regulation
4. Human Population Growth
3. Community Ecology
1. Community Ecology
4. Ecological Research
1. Ecosystem Experimentation and Modeling
2. Nitrogen and Phosphorus Cycles
3. Freshwater Biomes
4. Population Growth Curves
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5. Introduction to Water Pollution
3. Module 3: Cell Biology
1. Introduction to Cell Biology
1. Introduction to Cells
. Prokaryotic Cells
. Eukaryotic Cells
. Protists
. Fungi
6. Eukaryotic Origins
2. Tour of the Cell: Water, Carbohydrates and Lipids
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1. Atoms, Isotopes, Ions, and Molecules: The Building
Blocks
. Water: the Molecule of Life
. Introduction to Biological Molecules
. Carbohydrates
. Lipids
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. Chemical Reactions of Biological Macromolecules
7. Components and Structure of Plasmal Membranes
3. Tour of the Cell: Proteins and Enzyme Function
1. Proteins
2. Enzymes
3. Buffers and Enzymes
4. Tour of the Cell: Nucleic Acids and Cell Cycle
1. Nucleic Acids and Nucleotides
. Cell Reproduction
. DNA Replication
. Prokaryotic Cell Division
. Eukaryotic Cell Cycle
6. Cancer and the Cell Cycle
4. Module 4: Genetics
1. Molecular Genetics: DNA to Protein to Phenotype
1. ‘Transcription
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2. Translation
3. Connection Between DNA and Phenotype
2. Meiosis and Mendelian Genetics
1. Sexual Reproduction
2. Meiosis
3. Mendel’s Experiments
4. Laws of Inheritance
3. Variations on Mendelian Genetics
1. Extensions of the Laws of Inheritance
4. Population Genetics
1. Population Evolution
2. Population Genetics
3. Formation of New Species
5. Module 5: Energetics
1. Cellular Energetics
1. Energy and Metabolism
. Thermodynamics
. Potential, Kinetic, and Free Energy
. Energy in Living Systems
. Cell Membranes and Passive Transport
6. Energy Requiring ‘Transport
2. Photosynthesis
1. Overview of Photosynthesis
2. The Light-Dependent Reactions
3. Calvin Cycle
3. Cellular Respiration
1. Overview of Cellular Respiration
2. Glycolysis
3. Oxidation of Pyruvate and the Krebs Cycle
4. Oxidative Phosphorylation
5. Metabolism Without Oxygen
4. Bacteria and Fungi: Using Alternative Energy Sources
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Metabolic Pathways
2. Prokaryote Structure
3. Prokaryotic diversity
4. Kingdom Fungi
6. Module 6: Plant Biology
1. Evolution and Diversity of Plants
1. Lichens, Protists and Green Algae
. Early Plant Life
. Bryophytes
. Seedless Vascular Plants
. Evolution of Seed Plants
. Gymnosperms
. Angiosperms
8. Asexual Reproduction
2. Plant Reproduction; Structure and Function of Plant
Tissues
1. The Plant Body
2. Plant Sensory Systems and Responses
3. Reproductive Development and Structure
4. Pollination and Fertilization
3. Interactions of Plants With Their Environment
1. Root and Leaf Structure
2. ‘Transport of Water and Solutes in Plants
3. Nutritional Requirements of Plants
4. Nutritional Adaptations of Plants
4. Photosynthesis, Global Climate Change, and Food
Production
1. Photosynthetic Pathways
2. Climate and the Effects of Global Climate Change
3. Human Population Continues to Grow
7. Module 7: Animal Biology
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1. Introduction to Animals
1. Features of the Animal Kingdom
2. Animal Tissue Types
3. Sponges and Cnidarians
4. Flatworms, Nematodes, and Arthropods
5. Mollusks and Annelids
6. Echinoderms and Chordates
7. Vertebrates
8. Homeostasis
2. Material Acquisition and Transport
1. Digestive Systems
2. Digestive System Processes
3. Nutrition
4. The Circulatory System
5. Systems of Gas Exchange
3. Internal Communication and Coordination
1. Nervous System
2. Endocrine System
3. Digestive System Regulation
4. How Animals Reproduce
4. External Communication and Coordination
1. The Integumentary System
. Sensory Systems
. Reflexes and Homeostasis
. Viruses
. Innate Immunity
6. Adaptive Immunity
5. Adaptations to Land
1. Urinary System
2. Musculoskeletal System
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Studio Biology - What is it?
An introduction to the format of Biology 198 - Principles of Biology, taught
at Kansas State University
The Studio Format
Introduction
"The first principle is that you must not fool yourself - and you are the
easiest person to fool." Richard Feynman, American physicist and Nobel
Prize winner, delivering the Caltech commencement address, 1974
Welcome to Principles of Biology, Kansas State University’s innovative
introductory biology course. Because this course is almost certainly unlike
any course you have taken before, we need to spend a little time to
introduce it, and tell you why this course is a great way to learn about
biology.
Unlike the traditional lecture & lab introductory biology courses at most
universities, Biology 198 at K-State is a studio-format course, combining
lecture and lab into the same class period. There are some unique things
about studio courses, and especially this one. Our studio model involves 2
separate 2-hour sessions per week, with a maximum of 78 students in the
studio; thus you will spend about 4 hours per week in the studio classroom.
So it is important to understand that you are in a studio course, which is not
a lecture, and not a lab, but is actually a hybrid of lecture and lab. Although
it is an introductory course, it was developed with input from all the faculty
members in the Division of Biology. There are usually two faculty
members, two GTAs and one or more undergraduate practicum student
instructors per 80 students in each section.
Why do we teach this course this way? Because we believe in education,
and also in giving KSU students a lot of education for their tuition dollars.
The studio format has been shown to be a very effective way for us to help
you learn about biology. In fact, it is about twice as effective as the
traditional lecture/lab course in terms of your learning and retention of the
material. So that’s why we teach it this way.
It is also unique in that the faculty members teaching this course can
include anyone in the department, including full professors. Introductory
science courses, in particular, tend to be taught by graduate teaching
assistants here, and at other institutions. If they are taught by a full
professor in Biology 198, many freshman students will not have another
course taught by a full professor until their junior or senior year. At many of
our peer institutions, introductory biology courses are taught with a single
instructor lecturing to 500-800 students, accompanied by a lab taught solely
with graduate students. That’s a relatively inexpensive way to teach
introductory science courses, but also a relatively ineffective way. If you
take advantage of the significant resources (both personnel and material)
that the Division of Biology devotes to this course, you will learn a lot of
biology. Equally importantly, you will learn how to study and be successful
in a university environment. That’s another advantage of the studio format!
Course materials
Two items are essential to your successful learning in this course, both of
which are designed to maximize learning in the studio environment. The
first is the free electronic textbook, which you are reading now. The second
is the Principles of Biology Studio Manual, which must be purchased from
the KSU Biology Graduate Student Association. It may look like a lab
notebook, but is actually something quite different. The studio manual is
analogous to your lecture notes in a standard lecture class; it is simply
YOUR record of what you do in the studio. What you see, do and hear
during your time in class will be recorded in your Principles of Biology
Studio Manual. More importantly, it is not analogous to a lab notebook ina
lab class. You do not need to turn it in to be graded (just like nobody grades
your lecture notes in a lecture class!). So please treat that studio manual,
which is a required text for this course, like you would your lecture notes in
any other class. Read it over before the next class, mark down any questions
you might have, and make sure you get a copy of the notes from another
student if you have to miss a studio class.
Course and testing structure
The course is divided into 7 units, each with four or five class periods that
are devoted to those units. There are tests on all 7 units, and the dates for
those tests can be found on your course syllabus (link). You will start with
an Introduction to Science and Biology (including two classes on
Evolution), then go immediately into the study of Ecology and Ecosystems.
After gaining this large-scale perspective, you will move to the study of
living things at the smallest scale (molecules and cells), and then move up
to the organism level (Genetics, Energetics). The final two units are more
traditional (Plant Biology, Animal Biology). The final exam, at the end of
the semester, is not a comprehensive exam; it covers only the last unit
(Animal Biology). But all of the learning that you have done in prior units
will be very important in your understanding of the concepts covered in that
final exam
The test questions are all written to evaluate your knowledge of the unit
Objectives. More importantly, the objectives for each class period are
provided to you at the very beginning of each section of the studio manual.
So if you want to know “What do I have to know for the tests?”, the simple
answer would be “the Objectives for that unit”. You will gain an
understanding of these objectives in many ways, not only from this
electronic textbook, but from the studio exercises, the web pages for this
class, and from discussions with your fellow students both inside and
outside the classroom. In addition we have prepared Study Guides that are
also based on the Objectives. For each of the day’s Objectives, we provide a
detailed listing of all the places (e.g. textbook, studio exercise, web page, or
some combination of those) where you can get the information needed to
master that Objective. If you spend your time in the studio wisely, and study
with those Study Guides regularly (not just the day before the exam!), you
should have a very clear understanding of the material that we think you
should be learning in this class. Each question on each exam is written with
one of those Objectives in mind, so it should be obvious that the Objectives
are the key item on which to focus your efforts.
Your responsibilities
There will be readings in the textbook for every class day (except for the
very first day of class); those reading assignments are listed in the Studio
Manual, right after the Objectives for every class period. The textbook
readings are an introduction to the topics for the studio exercises that day,
so you need to read them BEFORE coming to class each day. In order to
assure that you do the reading, there will be a short quiz over the reading
material for every class period. By the end of the semester, the points for
these quizzes add up to approximately the same value as a unit exam. The
points should provide some incentive, but as you learn more about this
course you should also figure out that learning in the studio classroom is
more efficient if you have a good understanding of the material covered in
the reading for that day. And more efficient learning in the classroom
translates to better scores on the unit exams!
In addition, your instructors will track your attendance in the studio;
attendance is strongly recommended for this class. Interacting with your
instructors and fellow students is an important component of the class, and
we have excellent data which prove that missing multiple classes is highly
correlated with lower exam scores, and lesser learning and retention. We
really want you to learn biology, but you can’t do that if you are not in
class. So to make sure that you take full advantage of the learning
opportunities in the studio, we give an attendance bonus at the end of the
semester. Please see the syllabus for more details.
Your success in this course, both in terms of amount learned and in terms of
a good grade, is assured if you understand the format of the course, do the
assigned readings and attend the studio sessions faithfully, and spend at
least as much time studying outside the classroom as you spend inside the
classroom. You are responsible for learning, just as you are responsible in
every class you take. But the difference in this class is that we do
everything we can to provide the resources and the environment where
learning is maximized.
Instructor responsibilities
Your studio instructors will deliver a brief (10-15 minute) introductory
lecture at the start of each class day, and an equally brief wrap-up session at
the end. In between those two lectures, you will be working with your
fellow students on the studio exercises for that day. During that time the
instructors will circulate in the studio, asking questions, answering
questions, and generally helping you learn the material. Please take
advantage of this incredible opportunity to interact, one on one, with your
faculty and GTA instructors. If you have a question, don’t be shy. If you
want to know if your class notes (i.e., the stuff you are writing in the Studio
Manual) are accurate, ask an instructor. Their job is to help you learn the
material, and they can help a lot more if they know what your questions and
concerns might be.
Your studio instructors will also be responsible for grading the daily quizzes
and recording those grades, usually in a course that they set up on K-State
Online. If you are not familiar with K-State Online, don’t worry. It is our
course Management system, and it is very easy to navigate. Your studio
instructors will not be responsible for writing the biweekly unit exams.
Since there are 10 sections of this course each semester, it is better (and
more fair) if all students in all sections take the same exams. So those
exams are written by the course coordinator, and all exam questions are
vetted by faculty members who are teaching in one or more sections in a
semester. The first 6 unit exams are administered on Monday evenings (see
syllabus for the exact dates), and the final unit exam is administered on
Thursday morning during finals week. Grades for these exams will be
recorded on K-State Online as well, so that you have ready access to your
grade information.
Helpful hints
¢ Read the assigned material before coming to class.
e Don’t skip class.
e Take advantage of the learning opportunities afforded in the studio
(your fellow students, the instructors, the practicum students, the
studio exercises, etc.) every time you are in class.
e Take good notes and read over your notes in the studio manual within
24 hours after every class.
e Use the study guides and concentrate on the Objectives when you
study for the unit exams.
e Study a little bit every day rather than cramming the day before the
exams.
e Ask lots of questions, and be prepared to answer lots of questions.
¢ Don’t fall behind, but if you do, make every effort to catch up as soon
as possible.
Science as a way of knowing
The scientific method as it applies to biology
Science as a way of knowing
"We absolutely must leave room for doubt or there is no progress and no
learning. There is no learning without having to pose a question. And a
question requires doubt. People search for certainty. But there is no
certainty." — physicist Richard Feynman, in a lecture at the Galileo
Symposium, 1964.
Introduction
What is “Science”? Everyone probably has some idea of what the word
means, but have you ever really thought about it? If so, here are some
questions to consider.
e Is science a body of knowledge?
e Is it the same thing as “truth”?
e Is it a way to understand everything, or just a few things?
e Is it a process, and if so, can everyone do it? Or do you have to be
highly intelligent, highly trained, or both, if you want to understand
science?
Hopefully by the end of this course, or even by the end of this first module,
you will have some good answers to those questions, and will be well on
your way to thinking like a scientist (at least for this class!). Let’s start with
the title of this chapter — Science as a Way of Knowing. That description is
from the title of a great little book by biologist John A. Moore, and is
actually a pretty good answer to the question of “What is Science?” Science
is both a body of knowledge, and an evidence-based process for generating
that knowledge. The word itself comes from a Latin term, scientia, which
means knowledge. But science is also about a particular kind of knowledge
- knowledge about the natural world. In addition, the process of “doing
science” can only help us gain additional understanding about the natural
world. It is of no use to us if we want to understand the supernatural. For
that we need other ways of knowing.
There are also some other aspects of science which you need to know, as
you move toward a better understanding of both the scientific knowledge
base and the scientific process.
Science
e requires interaction with the natural world in terms of observation,
detection, or measurement.
e is objective, or evidence-based; that evidence, or a repeated
demonstration of the evidence, must be available to everyone.
Scientists generally don’t just “take your word for it.”
e requires independent evaluation and replication by others.
e leads to conclusions that are always provisional, i.e., they will be
rejected or modified if new observations or measurements show that
they are false.
There are, of course, other "ways of knowing". How do we know what we
know? People who study knowledge (yes, there are such people, and they
are in the branch of philosophy known as epistemology) often classify that
knowledge based on the source of the knowledge. In mathematics and logic,
for example, we can point to things that we know are "rationally true". In
science, we focus on things that are "empirically true", i.e., based on
evidence that we can see, hear, touch, etc. In religion, and, to a lesser extent,
in history, we focus on "revelational truth", or knowledge that comes from
another source that we accept as true, based on our assessment of the
reliability of the source. So the subjects that you might study at this
university can depend on different sources for the knowledge that you will
be gaining. In this class we will focus, as noted above, on objective
evidence obtained from observations of the natural world, and we will use
some very specific terms to describe how those empirical observations form
the basis for scientific knowledge and understanding.
The process of science
So how does this process work? The processes that generate scientific
knowledge are known as the scientific method. But even as you learn this
method, it is important to realize that this is not a set recipe or process that
MUST be followed in all cases. The scientific method is best understood as
a statement of the core logical principles underlying how science works.
The process of science always uses these core logical principles, but any
individual scientific enterprise might not adhere exactly to the method
outlined below ([link]).
The Basic Scientific Method
Formulate
Hypotheses
I
Observation &
Experimentation
Accumulated Data
or observations
i" =
—
=> Theory
The Scientific Method — 1) Observations are used to formulate the
2) hypothesis, which is then 3) tested with experiments or new
observations. The 4) new data contribute to the pool of
observations, and also are used to refine the hypothesis as needed.
Eventually the accumulated data allow one to make a 5)
conclusion, which can contribute support for an existing 6) theory,
or in some cases, support for a new theory. In all cases theories
can be used to generate new testable hypotheses, which is why we
say theories are both explanatory and predictive.
All science starts with an observation, or set of observations, about the
natural world. You might observe a pair of male elk fighting in a high-
country meadow in Colorado, for example. The next step, if you want to
think about this scientifically, is to formulate some hypothesis to explain
that observation. A hypothesis is a statement that is simply an educated
guess about the cause(s) of the observed phenomenon. In order for that
hypothesis to be useful in a scientific sense, however, it must have some
additional characters. A scientific hypothesis must be testable, and it must
be falsifiable. It does no good to generate a hypothesis that you cannot test
in the real world. Thus it would not be a scientific hypothesis if you stated
that the elk were fighting because invisible men in an invisible spaceship
parked on the far side of the moon were controlling these elk with
undetectable brain waves. That might be the actual explanation, but you
can’t test it, and you can’t falsify it.
A good scientific hypothesis lends itself to making testable predictions; if
the hypothesis is true, then X must be true. In this case you might state
generate this hypothesis — these are male elk, and they are fighting for
control of a herd of female elk. Immediately some predictions come to
mind. If this hypothesis is true, you should be able to detect that these are
male elk. Without getting too close, you can see that they have antlers, and
previous work by other scientists (part of the set of accumulated
observations that you are relying on) has shown that only male elk have
antlers. Prediction confirmed. Another prediction might be that there should
be one or more female elk nearby, and that these females would eventually
go with the male who wins the fight or drives off the other male. You look
around, and you see a herd of 10 or so female (antlerless) elk watching the
spectacle. Another prediction confirmed. You will have to wait until the
fight is over before you know if the prediction about the females staying
with the winner is confirmed. But you have two predictions confirmed, and
so far your hypothesis is supported by the evidence. More importantly, it
has not been falsified. All of the data so far support it.
This brings up another important aspect of the process of science. In this
case you made predictions and confirmed them with additional
observations. You didn’t do anything to the subjects; you merely observed
them more closely. That is a valid approach. An equally valid approach
would be to test your hypothesis by means of experiments. Experiments
are manipulations of the experimental system, followed by additional
observations. In this case, for example, you might hypothesize that the male
hormone testosterone is causing the elk to fight. One prediction from that
hypothesis would be that injection of testosterone into female elk (which
don’t normally produce testosterone) would lead to aggressive behaviors in
the female elk. You would also predict that male elk, deprived of
testosterone, would be less aggressive. You might be able to come up with
some other predictions from this hypothesis that could be tested with other
experiments. You would have to capture some elk (male and female) to do
the experiments needed to test these predictions, of course. That could be
tricky, or dangerous, and you might need to hire and train help. Or you
could look for similar behaviors in smaller, more easily handled animals
such as mice or rats, and do the same experiments with those creatures.
Both of these approaches, using observations or using experiments, are
scientifically valid, as long as your hypothesis is testable and falsifiable.
Furthermore, as you will learn many times in this course, there are other
aspects of the experimental approach, involving concepts like sample size,
variables, and controls, which you will need to consider as well. We’ |l
save the discussion of those until a bit later, after we conclude our
consideration of the general scientific method.
If you look at ({link]), you will see that multiple tests of the predictions lead
to an increase in the number of observations. Any test of the hypothesis, no
matter if it confirms or disconfirms the hypothesis, adds to our knowledge
base. Generating new knowledge is one of the exciting parts of doing
science, in fact. All of these observations can be used by future generations
of scientists to test future hypotheses.
You’ll also find another important word in ({link]), and that is the word
theory. In regular conversations, people outside of science often use this
word to mean an unproven or unsupported explanation, a wild guess. As
you learned above, in science that description would be more appropriate
for the word hypothesis. In science, a theory means something quite
different. A theory is a statement or set of statements that explains some
aspect of the natural world that is supported by substantial amounts of data
from diverse lines of investigation. The statements that form a theory are
NOT "wild Guesses" but are often hypotheses that have been tested many
times. Therefore, a theory has predictive power and those predictions can be
tested. If a prediction is falsified, it does not mean the theory is false, it
means the hypothesis needs to be reworked. There are many theories in
science; examples relevant to the study of biology include the germ theory,
the cell theory, plate-tectonic theory, and of course the grand unifying
theory of evolution. All of them are well supported by incredible numbers
of observations; all of them are considered the best available explanation
for a diverse set of observations.
In addition, as shown in ({link]), you can see that just as observations lead
to predictive hypotheses, theories can lead to predictive hypotheses as
well. In fact, one of the hallmarks of a theory is that it provides a solid
framework for generating hypotheses and making predictions. Scientists are
confident in the explanatory power of theories, and thus are comfortable in
using them to construct hypotheses, design experiments, and frame the
interpretation of the data generated by those experiments. Just as a scientific
hypothesis is useless if it cannot generate predictive hypotheses, a theory
must serve as a framework for hypothesis building and testing. And just as
the predictions of the hypothesis must be borne out by new observations if
the hypothesis is going to be accepted, predictions from a theory must be
supported by the observations if the theory is to continue to serve as the
best available explanation for a vast set of observations.
Not shown in that figure, but implied nonetheless, is the fact that the
observations must be repeatable. Other scientists, working in other
locations, need to be able to do similar experiments and get the same
results. That is what is meant by the statement that science is objective, not
subjective. Another scientist has to be able to get the same results as you,
and vice versa. Again, the history of science has thousands of examples
where a new and exciting result was announced, but eventually forgotten
when other scientists could not get the same result. Recent ones include the
phenomenon known as “cold fusion”, or the identification of a virus that
was thought to cause Chronic Fatigue Syndrome (CFS). In all of these cases
the original observation was found to be flawed in some way, and
subsequent work, either by the original observers or by others, revealed the
flaws and debunked the explanation.
Finally, it is important to remember that all scientific conclusions are
provisional. In other words, a scientific conclusion is accepted as the
current best explanation, but with the understanding that future
investigators could make observations that might negate or modify the
conclusion. So it is likely that some of the things that you will learn in this
class are wrong, or at least incomplete. We still expect you to learn them,
since they are the current best explanation, but it is almost certain that
something in this textbook, or in the other materials for this course, will be
shown by future scientists to be erroneous or incomplete. Who knows, you
might be the scientist who does the work that reveals the error. Scientists
actually dream about being the person who overturns a long-established
notion, since that often means that their work will be remembered, and may
even appear in future biology textbooks. One example of overturning a
long-established concept, and ensuring a place in future textbooks, can be
found in Louis Pasteur’s experiments, described below
Experiments and controls
As mentioned above, a common approach to generate new scientific
knowledge is to perform experiments, where the scientist changes the
situation and then observes the effects of these changes. In keeping with the
scientific method, this starts with an observation, from which the scientist
generates a hypothesis. The hypothesis leads to a testable prediction,
followed by experiments based on that testable prediction. Let’s look at one
of the most famous experiments in all of biology as an example.
¢
| Broth without contamination without contamination
‘
‘Grgenismagrew | grew
Pasteur's test of the hypothesis of spontaneous generation [By
Carmel830 (Own work) [Public domain], via Wikimedia
Commons]. Pasteur attempted to explain the observation that
organisms (molds and bacteria) appeared in meat broth that had
been boiled. His hypothesis was that these organisms came from
the air, rather than from spontaneous generation. That hypothesis
would predict that organisms would not appear if the meat broth
was not exposed to air. He boiled the broth in flasks with long
necks; air could not enter past the fluid that was left in a U-shaped
section of the neck of the flask. As a control he boiled broth in
other long-necked flasks, but then broke the necks off so that room
air (and any microbes in that air) could fall on the broth. No
organisms grew in the flasks with intact necks; organisms were
found in abundance in the flasks with the broken necks.
It was widely believed in ancient times that living things arose
spontaneously if conditions were right. One of the observations that led to
this belief was that molds, bacteria, maggots and other life forms appeared
if one left a piece of meat out in the air for a while. This concept of
spontaneous generation was tested in 1860 by Louis Pasteur, using an
experimental setup diagrammed above ((link]). Pasteur heated meat broth,
in glass flasks, to a temperature where he imagined that no living things
were left alive in the broth. If he left this broth out in the open, it developed
active bacterial and mold growth, an observation which was consistent with
the notion of spontaneous generation. But Pasteur, having recently learned
about microbes, suspected that the mold and bacteria arose not from
spontaneous generation, but from microbes present in the air. So he devised
a set of experiments to test this hypothesis: Living microbial cells present
on dust particles in the air are the source of the living cells growing in the
heated meat broth.
What prediction could one make with this hypothesis? You can probably
think of a couple, but the one that Pasteur came up with was that if the meat
broth was in a vessel which excluded cells dropping into it from the air
above, there would be no bacterial or mold growth in the broth. So he
heated batches of broth in long-necked glass flasks until he thought the
broth was sterilized, and also heated the necks of the flask to allow him to
bend them into an “S” shape. The ends of the flasks remained open to the
outside air, but dust settled in the trap in the neck of the flask and did not
reach the surface of the meat broth. In other experiments, he broke off the
neck after heating the flasks, allowing dust particles to settle on the broth,
or waited a few days and then tilted the flasks so that the broth came into
contact with the dust trapped in the bottom of the trap in the neck of the
flask. Then he observed the results. Just as importantly, he repeated the
experiments several times to make sure that his observations were correct.
We’ve already discussed the hypothesis, and one prediction, above. But
what are some other important aspects of this experimental approach? One
is the concept of a variable. A variable is some condition of the
experimental setup that can be manipulated by the experimenter. Ideally, the
experimenter should change only one variable at a time (keeping all other
conditions identical); this makes interpretation of the results a lot more
straightforward. What was the variable in Pasteur’s experimental setup? In
this case, the variable was access of dust to the surface of the broth. In
flasks that were left open, access was allowed. In the flasks that had an
intact S-shaped trap in the neck, access was not allowed. Pasteur also
manipulated this variable by tilting the S-shaped flasks so that accumulated
dust could contact the broth.
The other important part of this experimental approach is the concept of
control experiments, also known by a shorter term as just controls. A
control experiment is a setup where the variable is not introduced, so that it
can be directly compared to the experimental situation where the variable
(access of dust particles to the broth) is included. So a control experiment
for Pasteur's incubation of broth in an open-necked flask would be
incubation of broth in the S-necked flasks. If the variable is introduced by
tilting the flasks, the control would again be the S-necked flasks. All other
conditions (heating temperature, amount of broth, size of flasks, etc.) were
the same in the experimental and control situations. The only thing that was
different was a single variable (access of dust particles to the meat broth),
because that was the hypothesized source of the living cells that grow in
meat broth left out in the open. A single control experiment is usually all
that is needed if there is only a single experimental variable being
manipulated.
But it is not always possible to simplify a system so that there is only one
variable. In those cases, as you will learn in the studio exercises for this
class, you might need multiple control experiments. Experiments and
controls will also be repeated before the investigator reports the results. It
will be described in a way such that other investigators can readily repeat it
as well. In some situations the results will be subjected to statistical
analysis, although this was not necessary in Pasteur’s experiment. Statistical
analysis is critical in many scientific approaches, particularly in studies
involving hypotheses about human subjects (e.g., the hypothesis that
smoking causes lung cancer), where experimental manipulation of the
subjects is difficult or impossible. A scientific experiment, no matter how
the results are analyzed, should lead to a conclusion that either supports, or
fails to support, the hypothesis. Finally, the experimental results should lead
to additional hypotheses, and additional predictions, that can generate
further support (or lack of support) for the hypothesis. Try to think of a few
additional experiments that you might have suggested to Louis Pasteur if
you were alive in 1860, and if you could speak French!
Other aspects of science
The characteristics inherent in the scientific process lead to another
property of science, and that is that science is self-correcting. By that we
mean that errors can be made, but that continued application of the tools
and processes of science will usually lead to elimination of the errors and a
more accurate understanding of the natural world. Science never really and
finally proves anything to be true; it can, however, prove things to be
untrue. To some people, in fact, that characteristic of science, its fluid and
changing nature, is maddening. If you require solid ground to stand on, and
immutable truth in all aspects of your life, you probably shouldn’t become a
scientist. If you find excitement in being part of an enterprise that is
constantly changing the extent, and even the nature, of knowledge, then you
have some of what it takes to be a scientist. But even if you don’t become a
scientist, a bit on scientific knowledge, and a bit of practice with the
scientific process, will help you understand the things you need to
understand in order to make intelligent decisions about many things, such
as health care, climate change, or other concepts that are in your future.
Science is also a curious mix of intuitive and counter-intuitive behaviors.
You practice the scientific method intuitively every day, whether you realize
it or not. If you flip on the light switch in your bathroom in the morning,
and the light doesn’t come on, you probably take a scientific approach to
solving that problem. You might hypothesize that the bulb is burnt out, and
if that hypothesis is correct, replacing the bulb should solve the problem. So
you do that experiment, and replace the bulb, and the light goes on, and you
can continue with your daily activities blissfully unaware of the fact that
you acted scientifically already that day. Intuitive science in action!
But some aspects of science, and particularly the scientific process, are not
intuitive. All of us have the ability to think that our explanation of some
phenomenon is correct, even if there are other observations that contradict
that explanation. In fact, we often search for additional evidence to confirm
our conclusion, and ignore any evidence that we might find that casts doubt
on the conclusion. This is known as confirmation bias, and is particularly
strong in situations where we have an large emotional or financial stake in
the conclusion. For example, you might consider yourself a pretty good
basketball player. So when you have missed 10 shots in a row, you keep
shooting until you make a shot, and then you feel better about your belief
that you are a good basketball player, even if those shooting percentages
contradict that belief. Or you might make a visit to the chiropractor when
your neck hurts, and the chiropractor might make your neck feel better. But
a few days later, when it hurts again, you might not take this as a sign that
chiropractic manipulation is not a cure. You might go back to that
chiropractor, to have the same manipulation, because you have already
invested money there, and you’d like to think that you are not wasting your
money. Confirmation bias, of the active sort rather than the passive version
in the previous examples, is particularly evident in people who buy into
conspiracy theories. They seek out others with the same beliefs, or they
only look at websites that are dedicated to that belief. It’s only human
nature that people like to hear what they think they already know. As a
character in Terry Pratchett’s Discworld series observes, “...what people
think they want is news, but what they really crave is olds...Not news but
olds, telling people that what they think they already know is true.” We all
like to think that we know everything that we need to know, and scientists
are no exception.
So scientists have to actively guard against confirmation bias. If a scientist
has an hypothesis, she has to come up with predictions and experiments that
will disprove that hypothesis. If the experiments indicate that the hypothesis
is wrong, the scientist has to abandon that hypothesis and generate a new
one, and it has to include the results of those disconfirming experiments.
This is a very difficult assignment, and certainly goes against lots of human
impulses. As the physicist Richard Feynman wrote, “The first principle is
that you must not foolyourself, and you are the easiest person to fool.”
Every good scientist has abandoned many more hypotheses than he or she
has confirmed; science teaches humility that way, for certain. Scientists
must be able to change their minds if observations warrant it; there is no
shame for a scientist who admits being wrong. Exactly the opposite, in fact.
There are many sad examples of individuals who hung on to a hypothesis
too long, and ended up with a tarnished reputation. But as we all know,
admitting you are wrong is difficult for most people, and scientists are
human too.
The science of biology
It’s now time to shift from a discussion of science in general to the specific
scientific discipline that you will be learning about, biology. Biology is the
study of life. that naturally leads to the question — What is life? Suprisingly,
that has proven to be a difficult question to answer in just a few words!
Most textbook-level definitions of life are merely a list of characteristics;
anything that exhibits all of those characteristics is said to be alive. Here’s a
typical list.
Living things:
e Respond to the environment.
e Assimilate and use energy from their environment.
e Maintain a relatively constant internal environment, even as the
external environment changes (homeostasis).
e Reproduce (at the level of organisms) and can evolve (at the level of
populations).
e Are highly organized, relative to their environment.
These are general characteristics, and might describe all organisms, even
those which have not yet been discovered yet (e.g., those on other planets or
solar systems). Until those organisms are discovered and studied, however,
that statement is provisional. In addition, scientists have discovered that all
living things discovered to date (i.e., the ones on this planet).are composed
of one or more cells, and have DNA as their hereditary/genetic material.
Some textbooks include these characteristics in their definition of life as
well. More importantly, the commonality of DNA as the genetic molecule
in all known life forms is strong evidence that all living things on this
planet are related, i.e., they have a common ancestor. A putative common
ancestor was a prediction made by Charles Darwin when he elucidated his
theories about evolution and natural selection. The fact that his prediction
proved to be correct is one (of many) pieces of evidence that support that
theory. You’ll learn about some of the other evidence later in this course.
One productive way to study and understand living things is to recognize
that there is a biological hierarchy, which is basically an organizational
concept map that allows us to focus on various levels of life.
Biosphere Life on Earth
=
All the organisms plus
Ecosystem = bees ‘
ate i | physical components
cy
All the organisms of
a prairie: animal,
plant, fungus, etc.
Community
=
Population Bison population
=
Organism A bull bison
Organ System ‘ J Circulatory system
Heart
>is
Tissue Cardiac Muscle tissue
cs
Cell Cardiac Muscle cell
=
Macromolecule an Myosin V
Tt,
u oO
\n—t
Molecule H~ Non Amino acid (Valine)
tt H3C~ ~ CH;
oe?
{ / \ 4 .
Atom [( @ )F Nitrogen Atom
The organization of life. Work by Eva Horne.
This hierarchy ([link])extends from atoms and molecules, through cells,
tissues, organs, organ systems, organisms, populations, communities, and
ecosystems all the way to the biosphere (Planet Earth and the living
organisms populating it). Biologists often focus on one or another of these
levels, simply because it is far easier to study one level than to try to
understand the entire spectrum, and the interactions between those levels.
But all biologists recognize that there ARE many interactions between these
levels, and those interactions lead to some very interesting and important
processes as well.
Consideration of this hierarchy, coupled with the difficulty in coming up
with a simple definition of life, leads some scientists to another perspective
as well. These scientists argue that it is pointless to try to define life. If life
arose from self-replicating chemical systems, which is the working
hypothesis in the field of science known as abiogenesis, and if there is a
continuum running from atoms to molecules to cells, etc., then it is not
possible to point to some arbitrary place on the continuum and define it as
“living”. Nobel Prize-winning abiogenesis researcher Jack Szostak writes”
None of this matters, however, in terms of the fundamental scientific
questions concerning the transitions leading from chemistry to biology.”
Indeed, as you come to learn more about viruses in this course or elsewhere,
you will probably have some sympathy for this perspective. Are viruses
alive? Or would it be better to say that they are somewhere along this
continuum, and bypass that question altogether?
As you proceed to learn biology in the studio classroom this semester, you
will expand your understanding of the details underlying those
characteristics of living things. For example, in regard to organisms
responding to the environment, you will learn some of the ways that
bacteria, plants and animals sense and respond to environmental conditions.
You will learn how bacteria, plants and animals reproduce, and how that
process of reproduction is integral to the process of evolution. You will
learn about cells and tissues and organs, all of which are highly structured
and organized arrangements, and how energy is obtained and expended so
that these organized structures can be produced and maintained. Hopefully
you will come to the realization that life, in all of its diverse incarnations, is
amazing. Which is why biologists continue to study it!
Evolution
An introduction to evolutionary theory, summarizing some of the key lines
of evidence in support of the theory.
Evolution
"How stupid of me not to have thought of that." — Thomas Huxley, after
reading Darwin’s Origin (On the Origin of Species by Means of Natural
Selection, or the Preservation of Favoured Races in the Struggle for Life).
Introduction
What is Evolution? Surely everyone has heard the word, and perhaps a lot
of other words to describe it, but do you really know what that word means,
in the context of biology? Here are a few common notions about evolution.
How many do you agree with?
1. Evolution has never been observed directly.
2. Evolution is only a theory, and has not been shown to be a fact.
3. Evolution means that life originated, and living things change,
randomly.
4. Evolution is progress; organisms get “better” and more complicated
whenever evolution occurs.
. Evolution means that individual organisms change.
6. In order for evolution to occur, the offspring of some organisms will
have to be radically different from the parental organisms.
Ol
If you said that all of these statements are false, then you have a good
understanding of evolution. They are indeed all untrue. However, this is a
list of some fairly common misconceptions about evolution, and many
people in the world (and particularly in the USA) share one or more of
these misconceptions. It is likely that you think that some or all of these
statements are true. One of the hardest parts of learning is to undo a well-
established misconception, so if you do think that one (or more) of those
statements is true, this chapter might be a bit harder for you. But it will be
worth the effort, since, as you will learn below, evolution is the guiding
framework for modern biological science. Once you have a good
understanding of evolution, and the mechanisms that drive it, you will be
well-poised to learn and understand the biology that comes in the rest of
this course.
Evolution — what is it?
The biological world is extremely diverse. In fact, that is one of the most
powerful realizations that come from the study of biology, or even just from
being an observant person in the world. Living things range from the
microscopic bacteria to the immense blue whale. They have a diversity of
life styles and metabolic capacities, from photosynthetic creatures who can
make their own food from carbon dioxide gas, to predatory creatures, all the
way to parasitic creatures who have some of the most complicated life
styles of all. Within any one of these groups, there is also astounding
diversity. Open any field guide, whether for birds, mammals, flowering
plants, or mushrooms, and you will be confronted with an abundance of
colors, sizes, shapes and behaviors. Even within a single species, say Homo
sapiens, there is diversity. Look around your classroom and you will see
people with a wide variety of skin colors, hair colors, eye colors, heights
and weights. This diversity is a fact, and for many millennia, human beings
have been trying to come up with explanations for that well-observed fact.
You are probably familiar with some of these explanations. Many ancient
peoples imagined that the world was created in the form that exists now,
and that blue whales, pythons, and lilac bushes were created and unchanged
since that creation. This is known as typology; every species conforms to an
ideal and unchanging type, and all members of the species are true to that
type. Wolves are a type, and all wolves (within certain parameters) were
considered to be similar to all other wolves, but not similar to foxes, and
even less similar to lions. And all of these creatures had ancestors who were
also true to the type. Once it became clear that there had been creatures,
preserved in the fossil record, unlike any creatures seen today, other
explanations were needed to account for these new observations. When it
became clear, from geology, that the earth was very ancient, and had been
in existence for millions and even billions of years, other explanations
became even more satisfactory. When it became clear, from studies of
comparative anatomy, that many creatures shared anatomical and
developmental similarities, even though they were of different types, other
explanations became obvious.
We won’t go through the many explanations for the diversity of life that
have been proposed and been discarded over the centuries. There are lots of
places where you can read about that historical progression, and it is
interesting, for sure. Rather we will get to the explanation that is the most
widely accepted scientific explanation today, and show how this
explanation is supported by evidence, and also leads to predictive
hypotheses that can serve as a further test of the explanation. That
explanation is known as the Theory of Evolution.
So we have a lot of observations to explain, and in this case those
observations are that there are a lot of diverse organisms on the planet, and
that they change over time. Those are observed facts, and can be
categorized under the broad umbrella of "evolution". As discussed in the
previous chapter, theories are powerful frameworks for explaining
observations, and for making new predictions about the natural world. The
theory of evolution is no exception. It is important to understand (see myth
#2 in the list above) that evolution is an observable fact, and that
evolutionary theory (which is not the same thing) is the best current
explanation for those observable facts. Indeed, it is the most powerful
explanatory framework in biology today. Theodosius Dobzhansky, a famous
biologist, expressed this sentiment quite well when he wrote in 1973,
“Nothing in biology makes sense except in the light of evolution.” On a
daily basis, scientists around the world are using the theory of evolution to
generate hypotheses, to interpret conclusions, and to make contributions to
scientific knowledge. So let’s look at that powerful explanation in more
detail.
At its simplest, evolution is defined as “descent with modification”. That is
joined to another concept, natural selection, to give us the first expression
of the theory of evolution, published by Charles Darwin in 1859. Darwin’s
genius was in recognizing, and thoroughly explaining, that descent with
modification was a common phenomenon, and that selection, whether
natural or artificial (e.g. animal breeding) was an explanation for life’s
diversity. So let’s look more closely at natural selection, since Darwin
identified it as the engine that drives the process of evolution.
Natural selection (aka adaptive evolution) is, as Darwin pointed out 150+
years ago, analogous to the process by which animal breeders produce
animals with novel traits (aka artificial selection). For example, a pigeon
breeder might notice that one of his pigeons has an unusually large ruff of
feathers around its neck. He breeds this pigeon with another pigeon, and
selects the pigeons with the biggest ruffs from among the offspring to be the
parents of the next generation. After a few cycles of this, some of the
pigeon offspring will have very unusual and pronounced neck ruffs, and
will look nothing at all like the original pigeon ancestor in that regard
(figure 1, below). This common practice gets its name from the fact that the
breeder selects, or chooses, specific animals to be the parents of the next
generation. And it works; there are many examples where substantial
changes in animal appearance, or behavior, can be brought about in just a
few generations by applying this artificial method of selection.
Darwin's pigeons (Original line drawings from Darwin's
"Variation in Animals and Plants under Domestication", 1868).
The common ancestor for all of these fancy pigeons was the Rock
Pigeon (center). By selecting for unusual morphological
characteristics, pigeon breeders are able to develop all of these
unusual pigeons, and many more.
Darwin’s genius, and the source of Huxley’s self-disparaging statement at
the top of this chapter, was to recognize that this process could also occur in
the absence of an individual who did the selecting. Natural selection, the
idea for which Darwin is so famous, simply recognizes three well-known
observations and puts them into a context that generates evolutionary
change. Let’s look briefly at each of these three observations.
The first thing that Darwin postulated is that the variations seen in living
things are due, to a greater or lesser degree, to heritable factors. In other
words, there are heritable variations among the individuals in a population
of organisms. Let’s break down that term a bit, and look at each of the
words, using examples mostly from human populations.
Firstly, we know that there are variations among individuals in a
population. Look around your classroom, or at your family picture album.
You probably don’t look exactly like your brother or sister, and your mom
and dad don’t look exactly like your uncles or aunts. So even in situations
where the parents are the same, variation occurs among the offspring.
Variation is even greater in a population of individuals who don’t share the
same parents. Variation is normal, and easily observed.
What about that other word, heritable? Again we now know that many of
those variable traits are heritable, i.e. they are passed from one generation to
the next. In humans, eye color, hair color, height, etc. are all characteristics
that might be the same in you and your parents. If you have a dog or cat,
and that dog or cat has offspring, you can often see aspects of the offspring
(e.g. coat color, size) that are identical to those in the parental animal. One
likely explanation for that observation is that you and your parents have
some shared molecule or molecules that determine each of those traits. We
now know (but Darwin didn’t) that the molecule is DNA, about which you
will learn more later. On the other hand, some conditions are not heritable.
For example, if you have a cat that lost its tail in a horrible and noisy
accident involving a rocking chair and your 300-lb great-aunt, and if the cat
has kittens, those kittens will have normal tails. The rocking chair might
damage the cat’s tail, but not its DNA. At the time of Darwin, the
mechanisms of heritability were not known (he knew nothing about genes),
but everyone understood that some traits were heritable, and others were
not. So again, the heritable variation that is necessary for evolution to occur
is easily observed in the natural world.
The second thing that Darwin observed, and that was a huge factor in his
synthesis of these observations into his theory, is that not all of the
individuals in a given generation will survive and reproduce to the same
degree. Simple mathematics corroborates that. If all of the fruit flies from a
single pair of fruit flies survived and produced a maximal number of
offspring, after a mere 25 generations (which can take just a single year in
this species) that population of flies would fill a ball 96 million miles in
diameter, or more than the distance from the earth to the sun. Fruit flies
have been around for lots longer than a year, and you can still see the sun,
so obviously fruit flies do not all survive and reproduce.
Finally, the third condition necessitates that these heritable variations can
result in differences in survival or reproductive success. Again, there is
abundant evidence for that. Inherited human conditions that result in mental
retardation, or physical deformation, often mean that the affected individual
will not survive or reproduce. Medical intervention has, in some cases, been
able to counteract those disabilities and allow individuals with some
inherited conditions to survive and reproduce, but in previous generations,
or in populations of organisms that do not have access to medical care,
many heritable variations were not represented in the next generation
because the individuals with those variations simply did not reproduce.
So the model Darwin proposed is quite simple. If all of those conditions
were true, organisms with heritable variations that enhanced their chances
for survival and reproduction would be more likely to be among the parents
of the next generation, and the frequency of those organisms with those
particular heritable variations would increase in the next generation. This is
a simple idea, but it has many ramifications for the study of biology.
It seems clear, just from observations we all have made, that these three
conditions do pertain in the natural world. If that is the case, then the
process of natural selection could operate, and variations that resulted in
reproductive success would become more common in the population. It is
important to understand that this process is the result of an interaction
between the organisms and their environment. Over time, organisms that fit
better into that environment will become more abundant in the population,
and may eventually be the only organisms in the population. The term
fitness, in this context, simply is a measure of how well individuals with
certain traits survive and reproduce in a particular environment. The
environment is an incredibly important aspect of this process. If the
environment changes, organisms which were fit for the previous
environment may suddenly find themselves less well-adapted, and rare
organisms that were ill-adapted in the previous environment may suddenly
become more fit to that new environment. Fitness is relative, and the
environment is a major player in the determination of fitness.
In addition, consideration of these processes in the real world leads to a
better understanding of the questions in the introduction to this chapter. As
you can see, the process of evolution is NOT random; the interaction of the
organism and its environment leads to selection, and selection, by the very
nature of the word, is not random. Just as an animal breeder chooses
specific individuals as the parents of the next generation, the process of
natural selection chooses specific individuals as the parents of the next
generation, leading to evolution of the population. There are some
important differences, however. In artificial selection, the breeder has a goal
(e.g. to get a goat that produces more milk), and designs the breeding
program with that goal in mind. In natural selection, there is no ultimate
goal, and no plan; organisms are selected for their adaptation in a particular
environment, which can (and often does) change. The process is unguided,
in the sense that there is no goal in mind, but unguided is not the same thing
as random.
Secondly, careful consideration of this process also disproves the notion
that evolution equals progress toward a “better” organism. An organism that
is better adapted to one environment can be very ill-adapted if the
environment changes. In that situation, a “worse” organism, one that is rare
in the first environment, is now the “better” one in the new environment.
That is not progress, it is just change. In fact, some organisms become so
well-adapted to their environments that they lose some of the complex
structures or pathways that their ancestors had. Cave fish have no eyes,
even though their ancestors did. Whales have no legs, even though their
ancestors did. These highly-adapted organisms are actually less complex
than the ancestors from which they evolved. Evolution clearly is not a
synonym for progress!
Finally, it should be clear that evolution is a change at the level of the
population, and not at the level of the organism. Natural selection acts on
organisms, but the result of selection is seen in the next generation. And this
change is usually very gradual; there is no need to invoke absurd situations
where a Cat gives birth to a dog, or vice-versa.
Darwin correctly pointed out the analogies between this process of natural
selection and artificial selection, the well-known process that animal
breeders used to select for interesting or useful variants in animal species.
In other words, natural processes can generate the diversity we find in the
natural world if all of those conditions are true, and if there is sufficient
time to produce many generations. You will learn more in the studio
exercises about how even small differences in reproductive success can,
over time, lead to large changes in the characteristics of organisms in a
population. Small changes (one or two genes in organisms that still are
members of the same species) are sometimes described as micro-evolution.
Larger changes that result in different species, for example, are described as
macro-evolution. This is an artificial distinction, actually. Macro-evolution
is merely micro-evolution that has proceeded for a longer time. For a clever
graphical illustration of that, see figure 2 below.
We all can agree (save for the severely color blind) that this text is red.
We can also similarly agree that this text is blue.
If we have red text and decide to change it by just a small amount, the change might be barely noticeable, but still a
very small change. This, we will call our micro-evolution. Every word up to now can be considered red, with very
minute changes in the hue. If I keep typing long enough, would anyone be able to tell me, just by looking, at which
word or letter is this post no longer red, but actually purple or blue? All this micro-evolution keeps occurring in the
text, with it's tiny changes in hue, but ultimately, I end up with a completely different color. It's actually the difference
between what one would consider red and what one would consider purple (or a whole new species, in this analogy)
which is macro-evolution. See, the common misunderstanding is, that macro-evolution means a dog being a direct
offspring of some other different canine-like species, or even more stupidly, a cat coming from a dog. Well, that's not
what macro-evolution is. There is really only one distinction between micro-evolution and macro-evolution, and it's
the same distinction between their prefixes: micro and macro. Just like if something is microscopic or if something is
macroscopic. Microscopic usually requires a microscope to see it because it's so small, but the macroscopic are things
large enough to be seen by the common human eye. However, things of both size are completely visible and plainly
exist, and there are many things in this universe between both general sizes. So as you read this, can you tell me the
first word here that is blue, and not purple? After all, every change in color since the first word in this paragraph has
only micro-evolved from the color next to it, but we've managed to macro-evolve through 2 colors. This, hopefully,
will illustrate how it's illogical to believe that macro-evolution doesn't happen, even given time for enough micro-
evolution to occur.
So tell me -- what was the first purple word in the block of text above? What's the first blue word? Remember, if
macro-evolution simply can not happen then you're saying the words you are reading now are still red.
How very gradual changes can, over time, result in significant
changes: A textual example.
In summary, natural selection is a powerful agent, and recognition of this
process was a powerful insight. Darwin proposed his theory in 1859, and
elaborated on it in other books and other editions of the Origin of Species.
Since Darwin’s time, other scientists have identified other agents, in
addition to natural selection, that result in changes in the characteristics of a
population, and you will learn more about those in later chapters.
Additionally, other scientists made many predictions based on this
explanatory framework, and did many experiments to test those predictions.
Scientists are still engaged in that process today, and Darwin’s ideas have
been confirmed many times over, and even extended so that we understand
how the process works in much more detail than Darwin did. That is, as you
learned in the previous chapter, one hallmark of a great theory.
Evidence for Evolution
There are multiple lines of evidence, many of which were unimagined in
the time of Darwin, that support his explanation for the diversity of life. The
following is not meant to be an exhaustive cataloguing of that evidence.
Indeed, more evidence accumulates every day, making it impossible to
point out all of the threads in that fabric. It is also important to recognize
that the evidence doesn’t come just from biology. For example, as noted
above, Darwin’s explanation would require a lot of time and many
generations. If the earth was too young, none of this could have happened.
The sciences of physics and geology confirm that the earth is over 4.5
billion years old, which is plenty long enough for evolution to occur. The
fossil record, the research subject of geology and paleontology, also
provides substantial supporting evidence for Darwin’s big idea. The
discovery of continental drift, and the development of plate tectonic theory,
made sense of a lot of observations about both the fossil record and about
populations of living organisms. Let’s look at a few of the lines of evidence,
and see how they all weave together to make the coherent and elegant fabric
that is the hallmark of a good scientific theory.
The fossil record
In science, radically new explanations can only be successful when the
conventional explanations no longer explain all the observations. In the
history of biology, this was the situation in the early part of the nineteenth
century, when many interesting fossils were being discovered and carefully
scrutinized. It soon became apparent that fossils were indeed the remains of
once-living organisms, and that fossils in geologically younger strata
seemed to be both similar and different from those in older strata. The fossil
record showed that whole groups of organisms appeared and disappeared
during the history of the earth. Others seemed to be much the same in rocks
of different ages. Familiar organisms, particularly marine mollusks such as
clams and snails, could be found in older rocks, but in many cases these
organisms were not identical to the current organisms. Plant fossils told the
same story. The reigning explanation for the diversity of life, creation of all
these creatures at the same time and place, clearly did not explain these new
observations. Evolutionary theory was a much more satisfying scientific
explanation, and the development of that theory by Darwin and others
started at that time.
Since Darwin’s time the fossil record has become much more extensive,
and the evidence for this explanation has become much more well-
supported. Gaps in the fossil record that were pointed out by Darwin’s
contemporaries have been gradually filled in. Indeed, the sciences of
geology and paleontology, in combination with biology, have allowed
scientists to make predictions about where, exactly, particular fossils in
particular gaps should be found.
The most recent (and spectacular) example of this was the discovery of
fossilized remains of a creature that bridges the gap between fish and
amphibians, which the first four-legged creatures (aka tetrapods) to move
onto land. The fossil record, coupled with genetic evidence from modern-
day amphibians and fish, indicated that this transition to land occurred
about 375-400 million years ago. But only fish fossils, or amphibian fossils,
had ever been found. Logic dictates that there should be a transitional
creature, or “missing link” in popular jargon, which had characteristics of
both fish and amphibians. It was reasoned that creatures such as this, if they
existed, would probably live in shallow areas at the edge of seas or bays.
Geologists knew which particular rock formations resulted from those sort
of environments of that age, and so expeditions were dispatched to search
for such fossils in one of those geological formations. These rocks were
deposited in warm shallow tropical seas 375 million years ago, but are now,
as aresult of continental drift, located on Ellesmere Island in the Canadian
Arctic. In 2004 fossils were found in those rocks that elegantly fit that
prediction; the creature was named Tiktaalik roseae. (figure 3, below). The
genus name for this “fishapod” comes from the name of a fish and was
suggested by local Inuits on Ellesmere Island, and the specific epithet
“roseae” honors an anonymous donor who helped fund these grueling
expeditions to the high Arctic. Tiktaalik “fins” have basic wrist bones, but
no digits, or fingers. It is truly a missing link, and its discovery stems
directly from predictions made on the basis of previous scientific
observations, in a classic example of the power of the explanatory
framework known as the theory of evolution. Descriptions of the
expeditions, and lots more about the incredible insights that have come
from those fossils, can be found in a charming book called “Your Inner
Fish”, written by Neil Shubin and published in 2008.
“Fishapod” evolution (By Maija Karala (Own work) [CC-BY-
SA-3.0], via Wikimedia Commons. A cladogram showing the
evolution of tetrapods, using the best-known transitional fossils.
From bottom to top: Eusthenopteron, Panderichthys, Tiktaalik,
Acanthostega, Ichthyostega, Pederpes.
Comparative anatomy and embryology
At the same time that the fossil record was making some scientists scratch
their heads and question the creation explanation for the diversity of life,
other scientists were looking more closely at these fossils and at the bones
of existing organisms. These comparative anatomists also made
observations which were much more easily explained by the theory of
evolution. The different bones in fossil skulls, for example, could be
compared to the bones in modern skulls, allowing anatomists to discern that
the fossil skulls and the modern skulls had remarkable similarities in the
number and the position of the individual bones in the skull. Most of the
bones in a fossil fish skull have counterparts not only in modern fish skulls,
but in fossil and modern amphibian skulls, or fossil and modern reptile
skulls, and even fossil and modern mammal skulls. Occasionally the fossil
record shows us when a skull bone is added or one is lost, and also allows
us to track progressive modifications in the positions of these bones on the
skull surface. We can only understand these observations in the light of
evolutionary theory — if we conclude that the bones reflect the fact that each
kind of organism is descended from some other. Descent with modification
is the most satisfying scientific explanation for these observations.
The anatomy of modern organisms also reflects this common ancestry. The
limbs of all tetrapods contain a similar number and arrangement of bones,
even though the size and shape of the bones can vary greatly in different
organisms. For example, the two bones in your forearm, the radius and the
ulna, have counterparts in other mammals (figure 2.4), in reptiles, in birds,
and even in fossil dinosaurs and pleisiosaurs . If all of these structures were
specifically created for moving around in a different environment (e.g.
water for the plesiosaur and air for the bird or bat), simple engineering
principles would dictate that different structures would be more efficient in
those different situations. Yet the same structures, endlessly modified, are
found in all of them. The simplest explanation for this is that the organisms
share a common ancestor where that structure originated, and evolutionary
mechanisms resulted in the modifications in size and shape that we see
today. This phenomenon is known as homology; structures are said to be
homologous structures if they occupy similar positions and arise from a
common ancestral structure.
A B C D
Homologous bones in the forelimbs of four vertebrates (By
Petter Bockman, via Wikimedia Commons). A-human, B-dog, C-
bird, D-whale. The various colors indicate bones of various groups
(e.g. dark brown = bones of the fingers, yellw = bones of the wrist,
red = ulna, beige = radius, and light brown = humerus). The
various bones in the forelimbs of four vertebrates differ in size and
shape, resulting in very different morphologies of the forelimbs of
these organisms. But both the number of bones, and their position
relative to each other, are quite similar, as is their embryological
development. These homologous parts provided one of Darwin’s
arguments in support of his theory of evolution.
Even vertebrates who have lost these limbs in the course of evolution (e.g.
snakes) had similar structures prior to that evolutionary change. Figure
shows the fossilized remains of a creature (Tetrapodophis amplectus) that
lived in what is now Brazil 120 million years ago. It had a snake-like body
and may be the ancestor to all snakes, but it also had four small limbs. The
forelimb shown in that figure clearly has the humerus, radius, ulna and hand
bones that are found in modern vertebrates.
Homologous forelimb bones in a fossil snake
Forelimb of Tetrapodophis
amplectus, a four-legged snake
from the early Cretaceous (120
million years ago). Hu =
humerus, ra = radius, ul = ulna
and man = manus (hand).
Photo from Martil, D. et al,
Science 349:416-19 (2015).
Embryologists also made predictions based on this evolutionary
explanation. They predicted that homologous bones would arise from
similar structures during the development of the embryo. For example, the
forearm bone that we call the radius, which looks radically different in the
forearms of a bat or a human or a mouse or a bird, would come from similar
structures in the embryos of bats, humans, mice or birds. Those predictions
also were found to be correct. So homology argues strongly for an
explanation that invokes descent with modification.
In contrast, the wings of insects and the wings of bats or birds do not have
similar structures, although they have similar functions (to propel the
organism through the air). These structures are said to be analogous rather
than homologous; they share a function but do not arise from a structure
that is found in a common ancestor. Indeed, if organisms predominantly had
analogous structures, which would be different engineering solutions to a
common problem, that evidence would be more consistent with the
explanation of independent creation of those organisms. But homologous
structures seem to be the much more common observation, making descent
with modification a much more scientifically satisfying explanation.
Comparative biochemistry
One of the biggest surprises of modern biology came from the field of
science known as biochemistry. Once biochemists started to unravel the
mysteries of metabolism, the unity of life on this planet became quite
obvious. Creatures with incredibly different morphologies, habitats, and
lifestyles all seem to have incredibly similar metabolic pathways. Bacteria,
bonobos, bats and bananas all use a molecule known as ATP (adenosine
triphosphate) to store and provide energy within their cells, for example.
The metabolic pathway known as glycolysis, which you will learn about in
subsequent chapters, is found in all the organisms on the planet, and the
enzymes that are used in that pathway are quite similar in these diverse
organisms. Again, this argues strongly for common ancestry, which is a
strong prediction that arises from a “descent with modification”
explanation. Once an ancient cell developed these metabolic pathways,
there was no need to re-invent that wheel. It is somewhat ironic that some
of the best evidence for a particular explanation for the diversity of life
comes from the discovery of the unity of life at the molecular level.
Genetics and genomics
Besides ATP, another molecule common to all life forms on the planet is
DNA (deoxyribonucleic acid). This molecule stores genetic information, so
it is the molecule of heredity. Its role in heredity also means that it can be
modified under some circumstances, thus giving rise to the variations
described above. Darwin knew nothing about DNA when he proposed his
theory in 1859; his ideas about mechanisms of heredity were, in fact,
spectacularly wrong. But the discovery of the mechanisms of heredity,
starting with Mendel in 1866, and extended by many others in the early part
of the 20" century, made it possible to finally propose mechanisms by
which heritable variations arise and are transmitted between generations. In
fact, the first 4 decades of the 20" century were the years when the two
seemingly unrelated fields of genetics and evolution were united. This Neo-
Darwinian synthesis, starring Theodosius Dobzhansky, Ernst Mayr, and
George Gaylord Simpson, resulted in modern evolutionary theory, and
allowed scientists from both genetics and evolutionary backgrounds to work
together to make and test predictions.
The elucidation of the structure of DNA by Watson and Crick in 1953,
followed soon by the breaking of the genetic code, provided even more
evidence for descent with modification. DNA, as you will learn later,
functions as a repository of information. In order for the information to be
used to build a cell or an organism, it must be read and translated into
different molecules. The processes, and the enzymes, that do this work of
reading and translating are virtually identical in all living creatures on the
planet. The genetic code was, perhaps prematurely, called the “universal”
genetic code for precisely that reason; it is translated identically in almost
all organisms that have been discovered to date. Once again, this is a strong
argument for common ancestry and descent with modification.
But the really impressive outcome of this fusion of molecular knowledge
and organismal knowledge comes from the study of the structure of genes,
and genomes, at a detailed level. Incredibly, scientists have discovered
molecular fossils of a sort — stretches of DNA which are not used in modern
organisms, but which remain in the genome as a record of functions in the
past. For example, chickens don’t have teeth, but they have genes for tooth
proteins, turned off long ago, still lurking in their genomes. Those genes
can be turned on under the right conditions, producing toothy structures,
which were last seen in dinosaurs, the extinct ancestors of modern chickens.
There is no good explanation for these observations, other than descent with
modification. Similarly, detailed analysis of the DNA of organisms,
including now some long-dead organisms like mammoths and
Neanderthals, allows scientists to test predictions about common ancestry,
and gain insights into the course of evolutionary change in all organisms. In
fact, evidence from analysis of DNA, and other molecules, has allowed us
to fine-tune our hypotheses about ancestry and relationships throughout the
biological world, as explained in the next chapter on Taxonomy and
Phylogeny.
Taxonomy and phylogeny
An introduction to taxonomy and phylogeny
Taxonomy and Phylogeny
"Birds in a way resemble fishes. For birds have their wings in the upper part
of their bodies, and fishes have two fins in the front part of their bodies.
Birds have feet on their under part, and most fishes have a second pair of
fins in their under part...”" — Aristotle (384-322 B.C), De Incessu
Animalium.
Introduction — Differences and Similarities
Observations and speculations about the similarities and differences of the
life forms around us clearly have a long history. Aristotle’s ancient musings
about animals pre-date the concept of homologous and analogous
structures, which we discussed in the last chapter, but his insights are
accurate today. Aristotle was the first to write about his attempts to classify
animals into groups, and his classification scheme was the standard for
many centuries. Attempts to refine the classification of animals (and other
living things) continue even today, as you will see. Those classification
schemes, throughout the centuries, have used many different criteria for
separating living things into different groups. “How is this thing different
from this other thing?” has been the focus of many scientific endeavors.
But, as Aristotle recognized in the passage above, it is just as important to
ask about the similarities, and not just focus on the differences.
We use the words taxonomy or systematics to describe the activity of
classifying and naming living things. There are many ways to divide living
things into groups; the ability to recognize and classify things is a deeply-
seated and oft-used human activity. Some of these schemes are based on
habitat, e.g. water-dwelling creatures vs. land-dwelling creatures or aerial-
dwelling creatures. Others are based on internal characters. For example,
Aristotle’s two most basic groups were those with blood and those without
blood, a grouping scheme that coincidentally neatly separates most of the
vertebrates from most of the invertebrates. But most schemes have been
based on morphology, such as size, shape, number and proportion of
appendages, etc. This sort of classification seems to be easy enough to do,
but, as you will see later in this chapter, it can lead to some interesting
mistakes.
Finally, it is important to understand that all classification schemes should
be viewed as simply being hypotheses. Like any hypothesis, a
classification scheme should change, or even be discarded, if new
observations contradict the predictions of the hypothesis. This leads to some
frustration on the part of some students, because (again) they would like to
have some certainty about what they are learning. But a science where
everything is certain would be a dead and dusty science, which certainly
doesn’t describe the state of taxonomy today, or tomorrow.
A brief history of taxonomy
Domain - Eukarya
Kingdom - Animalia
Phylum - Chordata
Class - Aves
Order - Accipitriformes
Family - Accipitridae
Genus - Haliaetus
Species - leucocephalus
Taxonomic information for the Bald Eagle
(photo by D. A. Rintoul)
After Aristotle, there was not a lot of progress in taxonomy for many
centuries. In fact, there may have been negative progress for some of that
time, as Aristotle’s system was brushed aside or forgotten. But in the 1700’s
a Swedish biologist who went by the Latin name Carolus Linneaus
developed a system of biological classification that still underlies the
system used today. His big contribution to the discipline was to introduce
the concept of using two names to describe the smallest unit of
classification, the species. In the Linnean system, every organism has a
unique “scientific name”, consisting of a specific epithet preceded by a
name for the next highest level of classification, the genus (plural = genera).
Higher levels of classification included, in order above the genus, family,
order, class, phylum, and kingdom. Subsequently another top level, the
domain, was added to this hierarchy, giving us the classification scheme
shown above ((link]). This bald eagle has the scientific name Haliaetus
leucocephalus. There are 7 other members of the genus Haliaetus. The
genus is placed in the Family Accipitridae, in the Order Accipitriformes, in
the class Aves, in the Phylum Chordata, in the Kingdom Animalia, and in
the Domain Eukarya. Biologists refer to a group of organisms, at any level,
as a taxon (shorthand for taxonomic unit, plural = taxa). Thus a species is a
taxon, as is a Genus, or a Family, or an Order, etc.
There are an estimated 8-9 millions species on our planet. Every organism
that has been described fits somewhere in this classification scheme. You
can explore this in much more detail at the Tree of Life website. There you
will find information on the thousands of species that have been described
and named, as well as their currently assigned place in the taxonomic
scheme. It is also worth pointing out that the basic unit of this scheme, the
species, is not a well-defined term at all. There are multiple definitions of
species that you can find with just a minimal bit of effort, and none of them
is entirely satisfactory. Just as we learned about the definition of life, it is
sometimes difficult to pin down an exact point on a hierarchy. As you will
see from the material below, the problems with a definition of species might
be related to the fact that evolution is ongoing, and that some groups of
organisms are at different points on an evolutionary path at the present time.
However, if we ignore the vexing issue of figuring out a widely-accepted
definition for “species”, it is clear that a system based on this unit has
several advantages. One of the immediate advantages of the Linnean system
was that it allowed biologists to bypass the often confusing different
common names that are used in various parts of the world, or in various
languages. For example, the animal that is known as a moose in North
America is confusingly called an elk in Europe. But when you refer to this
creature by its scientific name (Alces alces), there is no confusion. That is
why scientific papers always include the two term scientific name for a
species. The hierarchical nature of the Linnean scheme is also useful,
allowing us to easily understand the levels of similarity at different levels in
the scheme. For example, organisms in the same genus can be very similar
to each other, and may even be difficult to tell apart unless you are an
expert. The similarity becomes less apparent for higher taxa; the class Aves
includes that Bald Eagle mentioned above as well as your pet parakeet,
which may screech like an eagle, but which is otherwise not very similar to
an eagle at all.
The original Linnean taxonomy was based, as noted above, primarily on
external morphology. It also relied on the obvious fact that organisms are
related to each other in many ways, and that some seem more closely
related than others. However, a system based solely on morphological
similarities and differences can lead to some interesting classification
errors. For example, Linneaus had one Phylum named Vermes (Latin for
“worms”). This obsolete taxon included animals that we now classify with
the mollusks, others that we now classify with the vertebrates, and still
others that we now classify with crustaceans, as well as those that are still
classified as worms. This reinforces two aspects of taxonomy that are
important to remember. The first is that taxonomic classification schemes
are merely hypotheses, and should be discarded or modified if newly
obtained information is not consistent with that hypothesis. The second is
that classification schemes based only on one type of information (in this
case, external morphology) can be quite mistaken. Using more than one
type of information will lead to better and more stable taxonomies.
Prior to Darwin’s time, classification was merely cataloging, and the
cataloging system used morphology as the key characteristic for
determining relationships. There is no theoretical basis for preferring one
morphological cataloging scheme over another, however. The concept of
evolution, and its prediction of common descent, provided that theoretical
basis. Relationships, based on common ancestry, should provide a more
accurate taxonomy. Besides being similar in size or shape, two organisms
that were most closely related should have a common ancestor in the more
recent past than would be the case for two less closely related organisms.
The evolutionary history of the taxa was valuable and necessary
information in this approach. The word for the determination of the
evolutionary history of a species or group of species is phylogenetics, and
the hypothesized evolutionary history and relationships of a species or
group of species is a phylogeny. It quickly became clear that a taxonomic
scheme that reflected phylogeny would be better than the arbitrary
morphology-based schemes of the past. However, at the time of Darwin,
and for many years thereafter, it was not exactly easy to discern the
evolutionary history of organisms. So the development of a true
phylogenetic taxonomy took a long time to develop, and, indeed, it is still
being developed.
Taxonomy should reflect phylogeny
MRCA —”
A simple phylogenetic tree. MRCA =
Most recent common ancestor
The current approach to determining relationships between two (or more)
groups of organisms is the construction of what are called phylogenetic
trees. Phylogenetic trees are hypothesized reconstructions of evolutionary
history. They depict arrays of extant (currently living) organisms at the tips
of the branches, and branch points that indicate a common ancestor. ({link]).
A, B, C, D, and E in this diagram are the species being considered. The
vertical axis represents the passage of time. The branch points represent
organisms that are putative common ancestors of the organisms on the
branches above. In some cases these ancestors are known species from the
fossil record. In most cases they are not. A common ancestor for all of these
organisms is the branch point above the root of the tree, known as the most
recent common ancestor (MRCA). These trees can be horizontal and
vertical arrangements, or diagonal arrangements, both of which are shown
here. The two arrangements, in this case, represent identical trees in terms
of the hypothesized relationships of species A, B, C, D, and E.
Another critical point about these trees is that if you rotate the structures,
using one of the branch points as a pivot, you don’t change the
relationships. So just like the two trees above, which show the same
relationships even though they are formatted differently, all of the trees in
Figure 4.3 ((link]) are essentially identical in terms of depicting the
relationships between the species A, B, C, and D. If you don’t see how that
is true, just concentrate on the relationships and the branch points rather
than on the sequence of species (A,B, C and D) shown across the tops of
these diagrams. That sequence is not important; the branch structure
underlying the sequence is what you will need to focus on.
ABDC ACDB BCDA CODBA
ir Ly ie
ABDC ACDB BCDA CODBA
YYW Y¥
Different depictions of the same
phylogenetic tree. All of these
depict the same relationships
between the organisms A, B, C and
D,
To generate these tree structures, taxonomists use multiple characteristics to
compare organisms, including external morphology, internal anatomy,
behaviors, biochemical pathways, etc. Aristotle and Linneaus relied
primarily on morphological characters (size and shape). However, as noted
above, taxonomic schemes derived from comparing only a few
characteristic can be very flawed. So modern taxonomists rely, if possible,
on many characters, and taxonomies are constantly revised if additional
characters are measured and included in the analysis. In addition, the
development of a method called cladistics has revolutionized taxonomic
thinking, and cladistics also depends on an understanding of evolutionary
relationships. A clade is a group of organisms that consists of a common
ancestor and all of its descendants. So another name for clade is a
monophyletic group. For example, birds (including the bald eagle and your
parakeet AND their ancestral organisms including one class of dinosaurs)
are a clade. Clades can contain any number of species, but that number
must include all of the descendants and the common ancestor. In the
example above, A, B, C, D and E, as well as the ancestors indicated by the
branch points, are a clade. A and B, plus their common ancestor, are also
considered to be a clade.
What's the difference between a phylogeny, a phylogenetic tree, and a
cladogram? For our purposes, there really isn't much of a difference. In this
class we will use these terms interchangeably — they all describe a tree
structure that represents the hypothesized evolutionary relationships within
a group of organisms, based on data derived from various sources. The
important things to remember are 1) organisms are related, and 2) that we
can represent our hypotheses about these relationships with tree structures.
Cladistics relies on classifying characteristics of organisms as either
ancestral or derived (another term that is sometimes used for ancestral
characters is primitive). Ancestral characters are those inherited attributes
that resemble those of an ancestor to the group. Derived characters are those
features that are different from features found in the ancestor. The
assumption of ancestral relationships in this approach is important, and
signifies yet another way that evolutionary theory is the framework for
understanding much of biology.
But how do you know which features are ancestral, and which are derived?
There are several ways to do that, but for your purposes, you can assume
that characters shared by all the organisms in the group are probably
ancestral. Other characters, not shared by all the organisms in the group, are
assumed to be derived. Lists of characters are generated, and used to
prepare a tree-like structure known as a cladogram.
The best way to illustrate this process is with an example or two. Here is a
table with some characters in rows and some organisms in columns. If there
is an “X” in the column for an organism, the organism has that particular
characteristic.
List of characteristics of a group of
animals that can be used to construct a
cladogram.
Which of these characters is common to all of these organisms? Obviously,
it is the notochord. Assume that is the ancestral condition, and thus it should
characterize the oldest ancestor at the base of any cladogram that you
construct. Now you need to determine what the first branch in the tree is
based on. That would be the character that is shared by all but one of these
organisms, the presence of jaws. If you continue this process, adding a
branch to the tree to depict groups that have, or do not have, a character,
you will generate this cladogram ([link]).
A cladogram constructed from the
data in the table above. Using the
character list in the table above,
and recognizing that the notochord
is common to all of these
organisms, a cladogram was
constructed, using the other
characteristics in that list. Each
shaded ellipse represents an
ancestor possessing that trait, while
the organism(s) on the opposite
branch lack that trait.
Now that you know how to construct one, there are a few other things about
cladograms that you need to know.
e The organisms along the top, or end, of a cladogram are not ordered in
any particular way, and are not ancestors of each other. The order does
not imply any sort of ranking from “primitive” to “advanced”. As
discussed in the previous chapter, evolution is not synonymous with
progress. As discussed above, the branches, and not the sequence of
organisms across the top, are the important information in these
diagrams.
e The most closely related organisms have the most recent common
ancestor, which is determined by counting the branch points backward
from the organisms aligned across the top. For example , the bald
Eagle and the Alligator have a more recent common ancestor than the
Alligator and the Antelope; the Bald Eagle and the Alligator are more
closely related than the Alligator and the Antelope.
e The lines between branches represents the arrow of time, but in most
cases the length of these lines is not directly related to the length of
time involved between the branch points. Some representations of
cladograms include an axis where time can be deduced, but if there is
no such axis, do not assume that a longer line represents a longer
length of time.
e There are many ways to represent a cladogram, and many of these may
look different, but will actually be identical. For example, the two
cladograms shown in figure 4.2 depict the same set of relationships,
even though one is vertically and horizontally aligned, and the other is
diagonal in nature. In both cases organism C is more closely related to
D (they share a relatively recent common ancestor) than A is related to
B (which share a less recent common ancestor).
Cladograms can be generated from any set of inherited characters. But they
become powerful tools, both for understanding the world and for generating
predictive hypotheses, when they include characters that we know are
quantitatively representative of relatedness, such as amino acid or nucleic
acid sequences. But the single most important character is one that most
directly reflects the degree of common ancestry — the DNA sequence. Since
(as you will learn in detail later) DNA is the molecule of “descent with
modification”, similarities and differences in DNA sequences from different
organisms are thus very useful in determining phylogenetic relationships.
The development of DNA sequencing technology has allowed scientists to
apply this tool to taxonomy, and this has resulted in an explosion of new
and exciting discoveries about phylogeny.
Morphological traits, such as those used to construct the cladogram above,
can be preserved in the fossil record, but DNA generally is not preserved.
However, since we know that your DNA was inherited from your parents,
and your grandparents, etc., we can predict that DNA sequences from
related individuals would contain evidence of that relatedness. These sorts
of “molecular fossils” can be used to produce and refine cladograms,
generating the structures we know as phylogenetic trees.
“This view of life”
It is important to also understand that phylogenetic trees are nested
hierarchies, i.e., any individual set of branches is also part of a larger set of
branches. This is easily seen in the accompanying figure ({link]). The clade
containing the eagle and the alligator nests within a clade that also contains
the antelope, and that clade nests within another clade, and another, etc. The
hypothesis of descent with modification (i.e. evolution) absolutely predicts
that the evolutionary history of organisms would be represented by a set of
nested hierarchies. Cladistic analyses, particularly those based on DNA
sequences, give results consistent with this prediction of Darwin’s theory.
Cladogram showing the nested
hierarchical arrangement of organisms
predicted by Darwin's theory of
evolution.
If we continue backward in time from any tip of any branch of the
phylogenetic tree above, we soon realize that all of these clades have a
common ancestor at some point in the distant past. DNA evidence supports
and strengthens this interpretation. As a matter of fact, the observation that
all life forms on the planet have DNA as their genetic material is further
support of this interpretation. The details of the arrangements of the various
branches may change, as new observations are included in the analyses of
relationships. The figure below ([link]) shows various phylogenetic trees
that have been used in the past. Note that the fundamental conclusion, that
all life on this planet came from a common ancestor, is a constant feature of
all of these trees. Indeed, as new observations are made, particularly in the
realm of DNA sequence data, this conclusion has become increasingly well-
supported.
Various depictions of the Tree of Life.
These hypothesized trees reflect the state
of knowledge at various times in the past.
As new observations are made, new
phylogenetic trees are constructed to
accommodate that new knowledge. It is
clear, from this example alone, that
scientific hypotheses change in response
to new discoveries and new knowledge.
The currently accepted Tree of Life [link]
will undoubtedly be modified in response
to new scientific discoveries in the future.
ARCHAEA - Color-enhanced scanning
electron micrograph of Pyrococcus furiosus,
Archaea are unicellular, do not have a cellular
nucleus, and can be heterotrophic or PROTIST (ciliate)-A composite of images FUNGI -A fruiting body (mushroom) of a ANIMAL -A Prothonotary Warbler
autotrophic. They are distinguished from of Stentor roeseli, Protists can be unicellular fungus in the Amazonian rainforest. Fungi (Protonotaria citrea) near Manhattan,
bacteria by a variety of characteristics, or multicellular, do have a cellular nucleus, can be unicellular or multicellular, do have KS. Animals are multicellular, nucleated,
including unique membrane lipids. and can be heterotrophic or autotrophic. a cellular nucleus, and are heterotrophic. and are heterotrophic.
Tree of Life
Bacteria Archaea Eukarya
Green
Filamentous Myxomycota
Spirochetes Bacteria Entamoebae Animals
Gram
positives
Methanosarcina
Methanobacterium Halophiles
Proteobacteria
Methanococcus
Planctomyces
Bacteroides
Cytophaga
Tricomonads
Microsporidia
| Thermotoga
Diplomonads
PLANT - Leavenworth’s Eryngo (Eryngium
leavenworthii) in the K-State University
Gardens. Plants are multicellular, nucleated,
and autotrophic.
in patient cerebrospinal fluid. Bacteria are
unicellular, do not have a cellular nucleus.
and can be heterotrophic or autotrophic.
The Tree of Life. The currently accepted hypothetical relationships
between the three domains of living things. Bacteria, Archaea, and
Eukarya (eukaryotes like you and me) are all thought to be descended
from a common ancestor that lived billions of years ago. Image
credits: Anthrax bacteria, from John A. Jernigan et al, "Bioterrorism-
Related Inhalational Anthrax: The First 10 Cases Reported in the
United States". Emerging Infectious Diseases 7(6), December 2001.
Pyrococcus furiosus, from Wikimedia Commons. By Fulvio314 (Own
work) (http://creativecommons.org/licenses/by-sa/3.0) Stentor,
copyright-free image from the Protist Image Database. Mushroom,
warbler, and eryngo are used with permission of the photographer,
David A. Rintoul.
The most widely accepted scheme has all living forms divided into three
major Domains, Bacteria, Archaea, and Eukarya. The evolutionary
relationship between these largest taxa is shown above ([link]). Note that
current data support the idea that the Eukarya (including me and you) are
more closely related to the Archaea than they are to the Bacteria; Archaea
and Eukarya have a more recent common ancestor compared to Bacteria
and Eukarya. Each of these Domains can be further subdivided into
Kingdoms, Phyla, Classes, Orders, Families, Genera, and Species. For
example, humans (Homo sapiens) are in the Domain Eukarya, Kingdom
Animalia, Phylum Chordata, Class Mammalia, Order Primates, Family
Hominidae, Genus Homo, and Species sapiens. In some cases these
classifications are further organized into taxa such as Superfamily, or
divided into taxa such as Suborder, but those are details that need not
concern us here.
Indeed, the entire Tree of Life is a nested hierarchy. We’re all related.
Darwin suspected this, and his theory predicted the phylogenetic trees that
scientists have generated from the observations and other data available to
us. In one of the most often-quoted passages from the Origin, he
demonstrates the sense of wonder that all biologists have when
contemplating the diversity of living forms.
"There is grandeur in this view of life, with its several powers, having been
originally breathed into a few forms or into one; and that, whilst this planet
has gone cycling on according to the fixed law of gravity, from so simple a
beginning endless forms most beautiful and most wonderful have been, and
are being, evolved." - Charles Darwin, 1859.
The Scope of Ecology
Introduction
""Ecology is the entire science of the relations of the organism to the
surrounding exterior world, to which relations we can count on the broader
sense all of the conditions of existence. These are partly of organic, partly
of inorganic nature... It is the "household' of nature."" - Ernst Haeckel,
1869, inventing and defining the word "ecology".
Ecology is the study of the interactions of living organisms with their
environment. The Greek root of the word, and the basis for Haeckel's
analogy above, is olKoc (oikos), which means house or dwelling-place.
Ecology simply means "knowledge of the house". One core goal of ecology
is to understand the distribution and abundance of living things in the
physical environment. Attainment of this goal requires the integration of
scientific disciplines inside and outside of biology, such as biochemistry,
physiology, evolution, biodiversity, molecular biology, geology, and
climatology. Some ecological research also applies aspects of chemistry and
physics, and it frequently uses mathematical models.
Levels of Ecological Study
When a discipline such as biology is studied, it is often helpful to subdivide
it into smaller, related areas. For instance, cell biologists interested in cell
signaling need to understand the chemistry of the signaling molecules
(which can be sugars, proteins, lipids, gases, or other compounds), as well
as the result of cell signaling. Ecologists interested in the factors that
influence the survival of an endangered species might use mathematical
models to predict how current conservation efforts affect endangered
organisms. To produce a sound set of management options, a conservation
biologist needs to collect accurate data, including current population size,
factors affecting reproduction (like physiology and behavior), habitat
requirements (such as plants and soils), and potential human influences on
the endangered population and its habitat (which might be derived through
studies in sociology and urban ecology). Within the discipline of ecology,
researchers work at four specific levels, sometimes discretely and
sometimes with overlap: organism, population, community, and ecosystem
((link]).
Organisms, Populations,
and Communities: Ina
forest, each pine tree is an
organism. Together, all the
pine trees make up a
population. All the plant and
animal species in the forest
comprise a community.
Ecosystems: This coastal
ecosystem in the
southeastern United States
includes living organisms
and the environment in
which they live.
The Biosphere:
Encompasses all the
ecosystems on Earth.
Ecologists study within several
biological levels of
organization. (credit
“organisms”: modification of
work by "Crystl"/Flickr; credit
“ecosystems”: modification of
work by Tom Carlisle, US Fish
and Wildlife Service
Headquarters; credit
“biosphere”: NASA)
Organismal Ecology
Researchers studying ecology at the organismal level are interested in the
adaptations that enable individuals to live in specific habitats. These
adaptations can be morphological, physiological, and behavioral. For
instance, the Karner blue butterfly (Lycaeides melissa samuelis) ({link]) is
considered a specialist because the females preferentially oviposit (that is,
lay eggs) on wild lupine. This preferential adaptation means that the Karner
blue butterfly is highly dependent on the presence of wild lupine plants for
its continued survival.
The Karner blue butterfly
(Lycaeides melissa samuelis)
is a rare butterfly that lives
only in open areas with few
trees or shrubs, such as pine
barrens and oak savannas. It
can only lay its eggs on
lupine plants. (credit:
modification of work by J &
K Hollingsworth, USFWS)
After hatching, the larval caterpillars emerge and spend four to six weeks
feeding solely on wild lupine ({link]). The caterpillars pupate (undergo
metamorphosis) and emerge as butterflies after about four weeks. The adult
butterflies feed on the nectar of flowers of wild lupine and other plant
species. A researcher interested in studying Karner blue butterflies at the
organismal level might, in addition to asking questions about egg laying,
also ask questions about the butterflies’ preferred temperature (a
physiological question), or the behavior of the caterpillars when they are at
different larval stages (a behavioral question).
The wild lupine
(Lupinus
perennis) is the
host plant for the
Karner blue
butterfly.
Population Ecology
A population is a group of interbreeding organisms that are members of the
same species living in the same area at the same time. A population is
identified, in part, by where it lives, and the area it occupies, which may
have natural or artificial boundaries. Natural boundaries might be rivers,
mountains, or deserts, while examples of artificial boundaries include
mowed grass, man-made structures, or roads. The study of population
ecology focuses on the number of individuals in an area and asks how and
why population size changes over time. Population ecologists are
particularly interested in counting the Karner blue butterfly, for example,
because it is classified as federally endangered. However, the distribution
and density of this species is highly influenced by the distribution and
abundance of wild lupine. Researchers might ask questions about the
factors leading to the decline of wild lupine and how these affect Karner
blue butterflies. For example, ecologists know that wild lupine thrives in
open areas where trees and shrubs are largely absent. In natural settings,
intermittent wildfires regularly remove trees and shrubs, helping to
maintain the open areas that wild lupine requires. Mathematical models can
be used to understand how wildfire suppression by humans has led to the
decline of this important plant for the Karner blue butterfly.
Community Ecology
A biological community consists of the populations of all the species
within an area, typically a three-dimensional space, and the interactions
within and among these species. Community ecologists are interested in the
processes driving these interactions and their consequences. Questions
about intraspecific interactions (interactions between members of the
Same species) often focus on competition among members of the same
species for a limited resource. Ecologists also study interactions between
members of different species; these are called interspecific interactions.
Examples of interspecific interactions include predation, parasitism,
herbivory, competition, and pollination. These interactions can have
regulating effects on population sizes, and can impact the ecological and
evolutionary processes, eventually affecting species diversity.
For example, Karner blue butterfly larvae form mutualistic relationships
with ants. Mutualism is a form of long-term relationship that has
coevolved between two species and from which each species benefits. For
mutualism to exist between individual organisms, each species must receive
some benefit from the other as a consequence of the relationship.
Researchers have shown that there is an increase in the probability of
survival when Karner blue butterfly larvae (caterpillars) are tended by ants.
This might be because the larvae spend less time in each life stage when
tended by ants, which provides an advantage for the larvae. Meanwhile, the
Karner blue butterfly larvae secrete a carbohydrate-rich substance that is an
important energy source for the ants. Both the Karner blue larvae and the
ants benefit from their interaction.
Ecosystem Ecology
Ecosystem ecology is an extension of organismal, population, and
community ecology. The ecosystem is composed of all the biotic
components (living things) in an area along with the abiotic components
(non-living things) of that area; this definition hearkens back to Haeckel's
original definition (above). Some of the abiotic components include air,
water, and soil. Ecosystem biologists ask questions about how nutrients and
energy are stored and how they move among organisms and the
surrounding atmosphere, soil, and water.
The Karner blue butterflies and wild lupine live in an oak-pine barren
habitat. This habitat is characterized by natural disturbance and nutrient-
poor soils that are low in nitrogen. The availability of nutrients is an
important factor in the distribution of the plants that live in this habitat.
Researchers interested in ecosystem ecology could ask questions about the
importance of limited resources and the movement of resources, such as
nutrients, through the biotic and abiotic portions of the ecosystem.
Note:
Career Connection
Ecologist
A career in ecology contributes to many facets of human society.
Ecologists can conduct their research in the laboratory and outside in
natural environments ([link]). These natural environments can be as close
to home as the stream running through your campus or as far away as the
hydrothermal vents at the bottom of the Pacific Ocean. Ecologists manage
natural resources such as white-tailed deer populations (Odocoileus
virginianus) for hunting or aspen (Populus spp.) timber stands for paper
production. Ecologists also work as educators who teach children and
adults at various institutions including universities, high schools, museums,
and nature centers. Ecologists may also work in advisory positions
assisting local, state, and federal policymakers to develop laws that are
ecologically sound, or they may develop those policies and legislation
themselves. To become an ecologist requires an undergraduate degree,
usually in a natural science. The undergraduate degree is often followed by
specialized training or an advanced degree, depending on the area of
ecology selected. Ecologists should also have a broad background in the
physical sciences, as well as a sound foundation in mathematics and
Statistics. But even if you don't plan to become an ecologist, understanding
ecological issues as a voter and citizen can help society meet the basic
human needs of food, shelter, and health care.
This landscape ecologist is releasing a black-footed ferret
(shown at right) into its native habitat as part of a study. (credit -
biologist photo: USFWS Mountain Prairie Region, NPS; black-
footed ferret photo, David A. Rintoul)
Ecology of Ecosystems
Introduction
"The early bird gets the worm, but the second mouse gets the cheese."
Willie Nelson, American musician
Competition for limited resources, whether it is a worm or a chunk of
cheese, is an essential component of the evolutionary mechanism we call
natural selection. Competition in communities (all living things within
specific habitats) is observed both between members of the same species,
and between members of different species. The resources for which
organisms compete include food (or sunlight in the case of plants), mineral
nutrients, nesting habitat, etc. Other critical factors influencing community
dynamics are the components of its physical and geographic environment: a
habitat’s latitude, amount of rainfall, topography (elevation), and
temperature. These are all important environmental variables that help
determine which organisms can exist within a particular area.
An ecosystem is a community of living organisms and their interactions
with their abiotic (non-living) environment. Ecosystems can be small, such
as the tide pools found near the rocky shores of many oceans, or large, such
as the Amazon Rainforest in Brazil ([link]).
(a) (b)
A (a) tidal pool ecosystem in Matinicus Island in
Maine is a small ecosystem, while the (b) Amazon
Rainforest in Brazil is a large ecosystem. (credit a:
modification of work by “takomabibelot’”/Flickr; credit
b: modification of work by Ivan Mlinaric)
There are three broad categories of ecosystems based on their general
environment: freshwater, ocean water, and terrestrial. Within these broad
categories are individual ecosystem types based on the organisms present
and the type of environmental habitat.
Ocean ecosystems are the most common, covering 75 percent of the Earth's
surface and consisting of two general types: shallow ocean (near islands and
continents), and the deep ocean. The shallow ocean ecosystems include
extremely biodiverse coral reef ecosystems. The surface water of the deep
ocean is known for its large numbers of plankton (small organisms that
disperse at the mercy of the winds and currents). Planktonic organisms can
be phytoplankton (photosynthetic organisms), or zooplankton (tiny animals
or animal larvae, which feed on the phytoplankton). These two
environments are globally important; the phytoplankton perform 40 percent
of all photosynthesis on the planet (i.e., produce 40% of the oxygen and fix
40% of the CO>). Although not as diverse as the other two, deep ocean
ecosystems contain a wide variety of marine organisms. Such ecosystems
exist even at the bottom of the ocean where light is unable to penetrate.
Freshwater ecosystems are the rarest, occurring on only 1.8 percent of the
Earth's surface. Lakes, rivers, streams, and springs comprise these systems;
they are quite diverse, and support a variety of fish, amphibians, reptiles,
insects, phytoplankton, fungi, and bacteria.
Terrestrial ecosystems, also known for their diversity, are grouped into large
categories called biomes, such as tropical rain forests, savannas, deserts,
coniferous forests, deciduous forests, and tundra. Grouping these
ecosystems into just a few biome categories obscures the great diversity of
the individual ecosystems within them. For example, there is great variation
in desert biomes: the saguaro cacti and other plant life in the Sonoran
Desert, in the United States and Mexico, are relatively abundant compared
to the lack of plant life in the desolate rocky desert of Boa Vista, an island
off the coast of Western Africa ([link]).
(b)
Desert ecosystems, like all ecosystems, can vary
greatly. The desert in (a) Saguaro National Park,
Arizona, has abundant plant life, while the rocky desert
of (b) Boa Vista island, Cape Verde, Africa, is devoid
of plant life. (credit a: modification of work by Jay
Galvin; credit b: modification of work by Ingo
Wolbern)
Ecosystems are complex with many interacting parts, and dissecting the
roles of these interacting components can be a challenge. Furthermore,
ecosystems are routinely exposed to various disturbances, or changes in the
environment that affect their compositions. For example, variations in
rainfall and temperature can affect patterns and rates of plant growth, even
though this may take several years. Many disturbances are a result of
natural processes. For example, fire is a disturbance that can be caused by a
lightning strike in a prairie or forest ecosystem. Recovery from disturbances
can be highly variable as well; some ecosystems (e.g. prairie) are adapted to
fire and can regenerate quickly. Others might recover more slowly. Other
disturbances are the result of human activities. The impact of environmental
disturbances caused by human activities is as important as the changes
wrought by natural processes. Human agricultural practices, air pollution,
acid rain, global deforestation, overfishing, eutrophication, oil spills, and
illegal dumping on land and into the ocean are disturbances, and biological
responses to these are of interest to ecologists and conservationists.
Equilibrium is the steady state of an ecosystem where all organisms are in
balance with their environment and with each other. In ecology, two
parameters are used to measure changes in ecosystems: resistance and
resilience. The ability of an ecosystem to remain at equilibrium in spite of
disturbances is called resistance. The speed at which an ecosystem recovers
equilibrium after being disturbed is its resilience. Ecosystem resistance and
resilience are especially important when considering human impact. The
nature of an ecosystem may change to such a degree that it can lose its
resilience entirely. This process can lead to the complete destruction or
irreversible altering of the ecosystem.
Food Chains and Food Webs
The term “food chain” is sometimes used metaphorically to describe human
social situations. In this sense, food chains are thought of as a competition
for survival, such as “who eats whom?” Someone eats and someone is
eaten. Therefore, it is not surprising that in our competitive “dog-eat-dog”
society, individuals who are considered successful are seen as being "at the
top of the food chain", consuming all others for their benefit, whereas the
less successful are seen as being at the bottom.
The scientific understanding of a food chain is more precise than in its
everyday usage. In ecology, a food chain is a linear sequence of organisms
through which nutrients and energy pass: primary producers, primary
consumers, and higher-level consumers are used to describe ecosystem
structure and dynamics. There is a single path through the chain. Each
organism in a food chain occupies what is called a trophic level (composed
of organisms that share the same function in the food chain and the same
nutritional relationship to the primary sources of energy). Depending on
their role as producers or consumers, species or groups of species can be
assigned to one or more trophic levels; for example bears eat plants (and
thus are primary consumers) and also eat other animals (and thus are
secondary or tertiary consumers).
In many ecosystems, the bottom of the food chain consists of
photosynthetic organisms (plants and/or phytoplankton), which are called
primary producers. The organisms that consume the primary producers
are herbivores: the primary consumers. Secondary consumers are usually
carnivores that eat the primary consumers. Tertiary consumers are
carnivores that eat other carnivores. Higher-level consumers feed on the
next lower tropic levels, and so on, up to the organisms at the top of the
food chain: the apex consumers. In the Lake Ontario food chain shown in
[link], the Chinook salmon is the apex consumer at the top of this food
chain.
One of the classes of consumers deserves special mention; these are the
decomposers, which break down waste or dead organic matter. Fungi and
bacteria are decomposers in many ecosystems, utilizing the chemical energy
in dead organic material to fuel their own metabolic processes. Some of the
decomposers are also known as detritivores (literally, detritus- or debris-
eaters). These are generally multicellular animals such as earthworms,
crabs, slugs, vultures, etc. which not only feed on dead organic matter, but
often fragment it as well, making it more available for bacterial or fungal
decomposers. These organisms have a critical role in ecosystems, and are
one of the main mechanisms by which nutrients get recycled for other
organisms to use again. Even apex consumers such as the Chinook salmon
have to die sometime, and the nutrients in their bodies can nourish a host of
detritivores and decomposers.
ORGANISM TROPHIC LEVEL
pst
ook salmon
Slimy sculpin
Mollusks
tt
Green algae
These are the trophic levels
of a food chain in Lake
Ontario at the United States-
Canada border. Energy and
nutrients flow from
photosynthetic green algae at
the bottom to the top of the
food chain: the introduced
Chinook salmon.
One major factor that limits the length of food chains is energy.
Approximately 90% of the energy entering the system (from sunlight
converted to carbohydrates by the primary producers) is lost as heat
between one trophic level to the next, as explained by the second law of
thermodynamics. Put another way, only 10% of the energy in a lower
trophic level is transferred to the next trophic level. Thus, after a limited
number of trophic levels (energy transfers), the amount of energy remaining
in the food chain may not be great enough to support viable populations at
yet a higher trophic level.
The loss of energy between trophic levels is illustrated by the pioneering
studies of Howard T. Odum in the Silver Springs, Florida, ecosystem in the
1940s ([link]). The primary producers contained 20,819 kcal/m?/yr
(kilocalories per square meter per year), the primary consumers contained
3368 kcal/m?/yr, the secondary consumers contained 383 kcal/m?/yr, and
the tertiary consumers only conained 21 kcal/m?/yr. Thus, there is little
energy remaining for another level of consumers in this ecosystem.
Tertiary consumers
Secondary consumers
Primary consumers
Primary producers
5,000 10,000 15,000
Energy content (kcal/m2/yr)
The relative energy in trophic levels in a Silver
Springs, Florida, ecosystem is shown. Each
trophic level has less energy available and
supports fewer organisms at the next level.
There is a one problem when using food chains to describe most
ecosystems. Even when all organisms are grouped into appropriate trophic
levels, some of these organisms can feed on species from more than one
trophic level, as noted above. Likewise, some of these organisms can be
eaten by species from multiple trophic levels. In other words, a strictly
linear model of ecosystems, the food chain, does not completely describe
ecosystem structure. A holistic model — which accounts for all the
interactions between different species and their complex interconnected
relationships with each other and with the environment — is a more
accurate and descriptive model for ecosystems. We call such models food
webs. A food web is a graphic representation of a holistic, non-linear web
of primary producers, primary consumers, and higher-level consumers used
to describe ecosystem structure and dynamics ([link]).
This food web shows the interactions between organisms across
trophic levels in the Lake Ontario ecosystem. Primary producers are
outlined in green, primary consumers in orange, secondary consumers
in blue, and tertiary consumers in purple. Arrows point from an
organism that is consumed to the organism that consumes it. Notice
how some lines point to more than one trophic level. For example, the
opossum shrimp eats both primary producers and primary consumers.
(credit. NOAA, GLERL)
A comparison of the two types of structural ecosystem models reveals
strengths for both models. Food chains are more flexible for analytical
modeling, are easier to follow, and are easier to experiment with, whereas
food web models more accurately represent ecosystem structure and
dynamics, and data can be directly used as input for simulation modeling.
Two general types of food webs are often shown interacting within a single
ecosystem. A grazing food web (such as the Lake Ontario food web in
[link]) has plants or other photosynthetic organisms at its base, followed by
herbivores and various carnivores. A detrital food web consists of a base of
organisms that feed on decaying organic matter (dead organisms), called
decomposers or detritivores. These organisms are usually bacteria or fungi
that recycle organic material back into the biotic part of the ecosystem as
they themselves are consumed by other organisms. As all ecosystems
require a method to recycle material from dead organisms, most grazing
food webs have an associated detrital food web. For example, in a meadow
ecosystem, plants may support a grazing food web of different organisms,
primary and other levels of consumers, while at the same time supporting a
detrital food web of bacteria, fungi, and detrivorous invertebrates feeding
off dead plants and animals.
Note:
Evolution Connection
Three-spined Stickleback
It is well established that changes in the environment play a major role in
the evolution of species within an ecosystem. However, little is known
about how the evolution of species within an ecosystem can alter the
ecosystem environment. In 2009, Dr. Luke Harmon, from the University of
Idaho in Moscow, published a paper that for the first time showed that the
evolution of organisms into subspecies can have direct effects on their
ecosystem environment.!{2mote]
Nature (Vol. 458, April 1, 2009)
The three-spine stickleback (Gasterosteus aculeatus) is a freshwater fish
that evolved from a saltwater fish. Evolutionary changes enabled it to live
in freshwater lakes about 10,000 years ago, which is considered a recent
development in evolutionary time ([link]). Over the last 10,000 years, these
freshwater fish then became isolated from each other in different lakes.
Depending on which lake population was studied, findings showed that
these sticklebacks then either remained as one species or evolved into two
species. The divergence of species occurred because different populations
used different areas of the lake for feeding.
Dr. Harmon and his team created artificial pond microcosms in 250-gallon
tanks and added muck from freshwater ponds as a source of zooplankton
and other invertebrates to sustain the fish. In different experimental tanks
they introduced one species of stickleback from either a single-species or
double-species lake.
Over time, the team observed that some of the tanks bloomed with algae
while others did not. This puzzled the scientists, and they decided to
measure some water quality parameters, including the amount of dissolved
organic carbon (DOC). DOC consists of organic compounds such as amino
acids, carbohydrates, lignins, and many others; these are usually derived
from decomposition of plant material in the water. DOC can vary not only
in composition, but also in the size of the particles. Larger aggregates of
decaying organic matter can give pond-water its slightly brownish color. It
turned out that the water from the tanks with two-species fish contained
larger particles of DOC (and hence darker water) than water with single-
species fish. This increase in DOC blocked the sunlight and prevented
algal blooming. Conversely, the water from the single-species tank
contained smaller DOC particles, allowing more sunlight penetration to
fuel the algal blooms. As the authors point out, "sticklebacks act as
ecosystem engineers, strongly affecting the composition of the DOC pool
and the physical light environment."
This change in the environment, which is due to the different feeding
habits of the stickleback species in each lake type, probably has a great
impact on the survival of other species in these ecosystems, especially
other photosynthetic organisms. Thus, the study shows that, at least in
these ecosystems, the environment and the evolution of populations have
reciprocal effects that may now be factored into simulation models.
The three-spined stickleback
evolved from a saltwater fish to
freshwater fish. (credit: Barrett
Paul, USFWS)
The Laws of Thermodynamics
Introduction
"Nothing in life is certain except death, taxes and the second law of
thermodynamics. All three are processes in which useful or accessible
forms of some quantity, such as energy or money, are transformed into
useless, inaccessible forms of the same quantity. That is not to say that these
three processes don't have fringe benefits: taxes pay for roads and schools;
the second law of thermodynamics drives cars, computers and metabolism;
and death, at the very least, opens up tenured faculty positions." Seth Lloyd,
Nature 430, 971 (26 August 2004)
Thermodynamics refers to the study of energy and energy transfer
involving physical matter. The matter and its environment relevant to a
particular case of energy transfer are classified as a system, and everything
outside of that system is called the surroundings. For instance, when heating
a pot of water on the stove, the system includes the stove, the pot, and the
water. Energy is transferred within the system (between the stove, pot, and
water). There are two types of systems: open and closed. An open system is
one in which energy can be transferred between the system and its
surroundings. The stovetop system is open because heat can be lost into the
air. A closed system is one that cannot transfer energy to its surroundings.
Biological organisms are open systems. Energy is exchanged between
them and their surroundings, as they consume energy-storing molecules and
release energy to the environment by doing work. Like all things in the
physical world, energy is subject to the laws of physics. The laws of
thermodynamics govern the transfer of energy in and among all systems in
the universe.
The First Law of Thermodynamics
The first law of thermodynamics deals with the total amount of energy in a
system. It states that the total amount of energy in a closed system is
constant. Energy exists in many different forms. According to the first law
of thermodynamics, energy may be transferred from place to place or
transformed into different forms within a system, but it cannot be created or
destroyed. This is the principle of conservation of energy. Transfers and
transformations of energy take place around us all the time. Light bulbs
transform electrical energy into light energy. Gas stoves transform chemical
energy from natural gas into heat energy. Plants perform one of the most
biologically useful energy transformations on earth: that of converting the
energy of sunlight into the chemical energy stored within organic
molecules. Some examples of energy transformations are shown in [link].
The challenge for all living organisms is to obtain energy from their
surroundings in forms that they can transfer or transform into usable energy
to do work. Living cells have evolved to meet this challenge very well.
Chemical energy stored within organic molecules such as sugars and fats is
transformed through a series of cellular chemical reactions into energy
within molecules of ATP. Energy in ATP molecules is easily accessible to
do work. Examples of the types of work performed by cells include
building complex molecules, transporting materials, powering the beating
motion of cilia or flagella, contracting muscle fibers to create movement,
and reproduction.
Chemical energy Light energy
>» >
Kinetic energy Chemical energy
Shown are two examples of
energy being transferred from
one system to another and
transformed from one form to
another. Humans can convert
the chemical energy in food,
like this ice cream cone, into
kinetic energy (the energy of
movement to ride a bicycle).
Plants can convert
electromagnetic radiation (light
energy) from the sun into
chemical energy. (credit “ice
cream”: modification of work
by D. Sharon Pruitt; credit “kids
on bikes”: modification of work
by Michelle Riggen-Ransom;
credit “leaf”: modification of
work by Cory Zanker)
The Second Law of Thermodynamics
A living cell’s primary tasks of obtaining, transforming, and using energy to
do work may seem simple. However, the second law of thermodynamics
explains why these tasks are harder than they appear. None of the energy
transfers we’ve discussed is completely 100 percent efficient. In every
energy transfer, some amount of energy is lost in a form that is unusable. In
most cases, this form is heat energy. Thermodynamically, heat energy is
defined as the energy transferred from one system to another that is not
doing work. For example, when an airplane flies through the air, some of
the energy of the flying plane is lost as heat energy due to friction with the
surrounding air. This friction actually heats the air by temporarily
increasing the speed of air molecules. Likewise, some energy is lost as heat
energy during cellular metabolic reactions. This is good for warm-blooded
creatures like us, because heat energy helps to maintain our body
temperature. Strictly speaking, no energy transfer is completely efficient,
because some energy is always lost in an unusable form.
An important concept in physical systems is that of order and disorder (also
known as randomness). The more energy that is lost by a system to its
surroundings, the less ordered and more random the system is. Scientists
refer to the measure of randomness or disorder within a system as entropy.
High entropy is a state with high disorder and low energy. To better
understand entropy, think of a student’s bedroom. If no energy or work were
put into it, the room would quickly become messy. It would exist in a very
disordered state, one of high entropy. Energy must be put into the system, in
the form of the student doing work and putting everything away, in order to
bring the room back to a state of cleanliness and order. This state is one of
low entropy. Similarly, a car or house must be constantly maintained with
work in order to keep it in an ordered state. Left alone, the entropy of the
house or car gradually increases through rust and degradation. Molecules
and chemical reactions have varying amounts of entropy as well. For
example, as chemical reactions reach a state of equilibrium, entropy
increases, and as molecules at a high concentration in one place diffuse and
spread out, entropy also increases.
Energy Flow
"All flesh is grass." - Isaiah 40:6
All living things require energy in one form or another. Energy is required
by most complex metabolic pathways (often in the form of adenosine
triphosphate, ATP), especially those responsible for building large
molecules from smaller compounds, and life itself is an energy-driven
process. Living organisms would not be able to assemble macromolecules
(proteins, lipids, nucleic acids, and complex carbohydrates) without a
constant energy input. And yes, Isaiah was correct; your flesh and all flesh
originated in the green plants of this planet.
It is important to understand how organisms acquire energy and how that
energy is passed from one organism to another through food webs and their
constituent food chains. Food webs illustrate how energy flows
directionally through ecosystems, including how efficiently organisms
acquire it, use it, and how much remains for use by other organisms of the
food web. The transfer of energy from one trophic level to the next is an
important concept when examining the effects of human disturbance on an
ecosystem.
How Organisms Acquire Energy in a Food Web
Energy is acquired by living things in three ways: photosynthesis,
chemosynthesis, and the consumption and digestion of other living or
previously living organisms. Organisms using the first two methods are
called autotrophs (auto=self, these organisms feed themselves). Those that
rely on consumption of others are called heterotrophs (hetero=other, these
organisms are fed by others). Photosynthetic autotrophs (photoautotrophs)
use sunlight as an energy source, whereas chemosynthetic autotrophs
(chemoautotrophs) use inorganic molecules as an energy source.
Autotrophs are critical for all ecosystems. Without these organisms, energy
would not be available to other living organisms and life itself would not be
possible.
Photoautotrophs, such as plants, algae, and photosynthetic bacteria, serve as
the energy source for a majority of the world’s ecosystems. These
ecosystems are often described by grazing food webs. Photoautotrophs
harness the solar energy of the sun by converting it to chemical energy in
the form of ATP (and NADP). The energy stored in ATP is used to
synthesize complex organic molecules, such as glucose.
Chemoautotrophs are primarily bacteria that are found in rare ecosystems
where sunlight is not available, such as in those associated with dark caves
or hydrothermal vents at the bottom of the ocean ({link]). Many
chemoautotrophs in hydrothermal vents use hydrogen sulfide (HS)
released from the vents as a source of chemical energy. This allows
chemoautotrophs to synthesize complex organic molecules, such as glucose,
for their own energy and in turn supplies energy to the rest of the
ecosystem, making chemoautotrophs the primary producers of their
ecosystem.
Swimming shrimp, a few squat lobsters,
and hundreds of vent mussels are seen at a
hydrothermal vent at the bottom of the
ocean. As no sunlight penetrates to this
depth, the ecosystem is supported by
chemoautotrophic bacteria and organic
material that sinks from the ocean’s
surface. This picture was taken in 2006 at
the submerged NW Eifuku volcano off
the coast of Japan by the National
Oceanic and Atmospheric Administration
(NOAA). The summit of this highly
active volcano lies 1535 m below the
surface.
Productivity within Trophic Levels
The general term "production" refers to the amount of new organic matter
generated by photosynthesis. Biologists have found it useful to define and
measure production more precisely. The total amount of solar energy
captured by photosynthesis is gross primary productivity or GPP.
Producers can use some of this energy for their own maintenance and
metabolism, and also use some to produce organic compounds that they
accumulate. This latter fraction is called net primary productivity or NPP.
This is the only energy, contained in the biomass of the producers, that is
available to all the heterotrophic organisms in that ecosystem.
Studies on both natural and agricultural systems have shown that plants
capture and convert about 1.3 - 1.6% of the solar energy that is available.
They use about a quarter of that captured energy for their own metabolism
and maintenance, leaving only about 1% of the solar energy as net primary
productivity. The standard unit for measuring productivity is grams of
biomass per square meter per year, but it is important to remember that this
biomass is actually converted to energy by the heterotrophic organisms.
Productivity in various ecosystems ranges from approximately 2,000
g/m?/yr in tropical forests, salt marches, etc., to less than 100 g/m?/yr in
some desert ecosystems. An example of gross primary productivity is
shown in the compartment diagram of energy flow within the Silver Springs
aquatic ecosystem ([link]). In this ecosystem, the total energy accumulated
by the primary producers (gross primary productivity) was shown to be
20,810 kcal/m?/yr.
Trophic levels in an aquatic ecosystem
Primary producers
13,187 20,810
7,618 4,250
2,265 3,368
1,103 720
Secondary consumers
272 383
to decomposers
Tertiary consumers
16 21
respiration + heat
Total heat and respiration
20,810
Gross productivity
Net productivity
Trophic levels and
energy flow in the
Silver Spring ecosystem
Modeling Ecosystems Energy Flow: Ecological Pyramids
The structure of ecosystems can be visualized with ecological pyramids,
which were first described by the pioneering studies of Charles Elton in the
1920s. Ecological pyramids show the relative amounts of various
parameters (such as number of organisms, energy, and biomass) across
trophic levels.
Pyramids of numbers can be either upright or inverted, depending on the
ecosystem. As shown in [link], typical grassland during the summer has a
base of many plants and the numbers of organisms decrease at each trophic
level. However, during the summer in a temperate forest, the base of the
pyramid consists of few trees compared with the number of primary
consumers, mostly insects. Because trees are large, they have great
photosynthetic capability, and dominate other plants in this ecosystem to
obtain sunlight. Even in smaller numbers, primary producers in forests are
still capable of supporting other trophic levels.
Another way to visualize ecosystem structure is with pyramids of biomass.
This pyramid measures the amount of energy converted into living tissue at
the different trophic levels. Using the Silver Springs ecosystem example,
these data exhibit an upright biomass pyramid ((link]), whereas the pyramid
from the English Channel example is inverted. The plants (primary
producers) of the Silver Springs ecosystem make up a large percentage of
the biomass found there. However, the phytoplankton in the English
Channel example make up less biomass than the primary consumers, the
zooplankton. As with inverted pyramids of numbers, this inverted pyramid
is not due to a lack of productivity from the primary producers, but results
from the high turnover rate of the phytoplankton. The phytoplankton are
consumed rapidly by the primary consumers, thus, minimizing their
biomass at any particular point in time. However, phytoplankton reproduce
quickly, thus they are able to support the rest of the ecosystem.
Pyramid ecosystem modeling can also be used to show energy flow through
the trophic levels. Notice that these numbers are the same as those used in
the energy flow compartment diagram in (({link]). Pyramids of energy are
always upright, and an ecosystem without sufficient primary productivity
cannot be supported. All types of ecological pyramids are useful for
characterizing ecosystem structure. However, in the study of energy flow
through the ecosystem, pyramids of energy are the most consistent and
representative models of ecosystem structure ({link]).
Note:
Ecological Pyramids
A. Biomass (dry mass, g/m2)
Silver Springs, Florida English Channel
Fishes 5
Decomposers Fishes 11 eee
baal acerca Herbivorous insects. 4
snails 37 ‘ Phytoplankton
B. Number of individuals per 0.1 hectare
Grassland (summer) Temperate forest (summer)
1 Bird
90,000 Predatory insects
200,000 Herbivorous
insects
200 trees
C. Energy (kcal/m2/yr)
Silver Springs, Florida
isl Tertiary (apex) consumer
Secondary consumer
Decomposers ] Eh
(fungi, bacteria)
5060
Fishes 21
Fishes 383 fa Primary consumer
Insects, snails °
3368 ica Primary producer
Ecological pyramids depict the (a) biomass, (b) number of
organisms, and (c) energy in each trophic level.
Consequences of Food Webs: Biological Magnification
One of the most important environmental consequences of ecosystem
dynamics is biological magnification. Biological magnification is the
increasing concentration of persistent, toxic substances in organisms at
higher trophic levels, from the primary producers to the apex consumers.
Many substances have been shown to bioaccumulate, including the
pesticide dichlorodiphenyltrichloroethane (DDT), which was first
publicized in the 1960s bestseller, Silent Spring, by Rachel Carson. DDT
was a commonly used pesticide before it became known that DDT and its
metabolites persist in ecosystems and organisms, and these compounds can
have harmful effects on many species in the higher trophic levels. In some
aquatic ecosystems, organisms in higher trophic levels consume many
individuals from the trophic level below. Small amounts of toxins in the
water become increasingly concentrated (magnified) from lower trophic
levels to higher trophic levels. So, DDT occurs in low concentrations in the
water is acquired by the producers, then magnified in the primary
consumers (small aquatic animals), then magnified again in the secondary
consumers (fish), and again in higher consumers such as fish-eating birds
(Ospreys, Pelicans, Bald Eagles). High levels of DDT metabolites cause the
eggshells of birds to become thin and fragile; they often crack or break long
before the baby bird hatches out. This effect resulted in significant declines
in populations of fish-eating birds. The use of DDT was banned in the
United States in the 1970s.
Other substances that biomagnify are polychlorinated biphenyls (PCBs),
which were used in coolant liquids in the United States until their use was
banned in 1979, and heavy metals, such as mercury, lead, and cadmium.
These substances were best studied in aquatic ecosystems, where fish
species at different trophic levels accumulate toxic substances that are
found in low concentrations in the primary producers. As illustrated in a
study performed by the National Oceanic and Atmospheric Administration
(NOAA) in the Saginaw Bay of Lake Huron ((link]), PCB concentrations
increased from the ecosystem’s primary producers (phytoplankton) through
the different trophic levels of fish species. The apex consumer (walleye) has
more than four times the amount of PCBs per gram, compared to
phytoplankton. Additionally, based on results from other studies, birds that
eat these fish may have PCB levels at least one order of magnitude higher
than those found in the lake fish.
ee
Rainbow Smelt /
Yellow
Perch
Alewife a
White Sucker
Phytoplankton
This chart shows the PCB
concentrations found at the
various trophic levels in the
Saginaw Bay ecosystem of Lake
Huron. Numbers on the x-axis
reflect enrichment with heavy
isotopes of nitrogen (1°N), which
is a marker for increasing trophic
level. Notice that the fish in the
higher trophic levels accumulate
more PCBs than those in lower
trophic levels. (credit: Patricia Van
Hoof, NOAA, GLERL)
Other concerns have been raised by the accumulation of heavy metals, such
as mercury and cadmium, in certain types of seafood. The United States
Environmental Protection Agency (EPA) recommends that pregnant women
and young children should not consume any top predator species such as
swordfish, shark, king mackerel, or tilefish, because of their high mercury
content. These individuals are advised to eat fish low in mercury: salmon,
tilapia, shrimp, pollock, and catfish, which are lower on the trophic
pyramids in their ecosystems. Biological magnification is a good example
of how ecosystem dynamics can affect our everyday lives, even influencing
the food we eat.
Biogeochemical Cycles
Energy flows, nutrients cycle
"We are stardust, we are golden, we are billion year old carbon." - Joni
Mitchell
Indeed, the elements that make up our bodies, and those of every other
living thing, were born in dying stars, billions of years ago. And energy
from our own star, the Sun, is an important player in making those elements
available to living organisms on this planet. Energy flows directionally
through ecosystems, entering as sunlight (or inorganic molecules for
chemoautotrophs) and leaving as heat during the many transfers between
trophic levels. However, the matter that makes up living organisms
(nutrients) is conserved and recycled. The five most common elements
associated with organic molecules—carbon, nitrogen, hydrogen, oxygen,
and phosphorus—take a variety of chemical forms and may exist for long
periods in the atmosphere, on land, in water, or beneath the Earth’s surface.
Geologic processes, such as weathering, erosion, water drainage, and the
subduction of the continental plates, all play a role in this recycling of
materials. Because geology and chemistry have major roles in the study of
this process, the recycling of inorganic matter between living organisms and
their environment is called a biogeochemical cycle. It is important to
understand that energy, flowing through ecosystems, is also needed to drive
biogeochemical cycles.
This image illustrates the flow of energy and the cycling of nutrients.
The dark green lines represent the movement of nutrients and the
dashed lines represent the movement of energy. As you can see,
nutrients remain within the system while energy enter via
photosynthesis and leaves the system primarily as heat energy, a non-
biolgically useful form of energy. Work by Eva Horne and Robert A.
Bear
Water contains hydrogen and oxygen, which are essential to all living
processes. The hydrosphere is the area of the Earth where water movement
and storage occurs: as liquid water on the surface and beneath the surface,
or frozen (rivers, lakes, oceans, groundwater, polar ice caps, and glaciers),
and as water vapor in the atmosphere. Carbon is found in all organic
macromolecules and is an important constituent of fossil fuels. Nitrogen is a
major component of nucleic acids and proteins and is critical to human
agriculture. Phosphorus, a major component of nucleic acids (along with
nitrogen), is also one of the main ingredients in artificial fertilizers used in
agriculture. Sulfur, an element that is involved in the 3—D folding of
proteins (as in disulfide binding), is released into the atmosphere by the
burning of fossil fuels, such as coal. Cycling and recycling of these
chemicals from the environment to organisms and back again is critically
important to all living things.
The cycling of these elements is interconnected. For example, the
movement of water is critical for the leaching of nitrogen and phosphate
into rivers, lakes, and oceans. Furthermore, the ocean itself is a major
reservoir for carbon. Thus, mineral nutrients are cycled, either rapidly or
slowly, through the entire biosphere, from one living organism to another,
and between the biotic and abiotic world.
The Water (Hydrologic) Cycle
Water is the basis of all living processes. The human body is more than 1/2
water and human cells are more than 70 percent water. Thus, most land
animals need a supply of fresh water to survive. However, when examining
the stores of water on Earth, 97.5 percent of it is non-potable salt water
({link]). Of the remaining water, 99 percent is locked underground as water
or as ice. Thus, less than 1 percent of fresh water is easily accessible from
lakes and rivers. Many living things, such as plants, animals, and fungi, are
dependent on the small amount of fresh surface water supply, a lack of
which can have massive effects on ecosystem dynamics. Humans, of
course, have developed technologies to increase water availability, such as
digging wells to harvest groundwater, storing rainwater, and using
desalination to obtain drinkable water from the ocean. Although this pursuit
of drinkable water has been ongoing throughout human history, the supply
of fresh water is still a major issue in modern times.
Freshwater 2.5%
(35,000,000 km?)
Lakes and rivers 0.3% ===
Groundwater (soil moisture, swamp
water, permafrost) 30.8%
Glaciers and permanent snow cover
68.9%
Only 2.5 percent of water on Earth is fresh water,
and less than 1 percent of fresh water is easily
accessible to living things.
Water cycling is extremely important to ecosystem dynamics. Water has a
major influence on climate and, thus, on the environments of ecosystems.
Most of the water on Earth is stored for long periods in the oceans,
underground, and as ice. [link] illustrates the average time that an individual
water molecule may spend in the Earth’s major water reservoirs. Residence
time is a measure of the average time an individual water molecule stays in
a particular reservoir. A large amount of the Earth’s water is locked in place
in these reservoirs as ice, beneath the ground, and in the ocean, and, thus, is
unavailable for short-term cycling (only surface water can evaporate).
Average Residence Time for Water Molecules
| Biospheric (in living organisms) 1 week
| Atmospheric 1.5 weeks
| Rivers 2 weeks
| Soil moisture 2 weeks—1 year
"Swamps 1-10 years
“Lakes & reservoirs 10 years
This graph shows the average
residence time for water molecules
in the Earth’s water reservoirs.
There are various processes that occur during the cycling of water, shown in
[link]. These processes include the following:
e evaporation/sublimation
¢ condensation/precipitation
e subsurface water flow
e surface runoff/snowmelt
e streamflow
The water cycle is driven by the sun’s energy as it warms the oceans and
other surface waters. This leads to the evaporation (water to water vapor) of
liquid surface water and the sublimation (ice to water vapor) of frozen
water, which deposits large amounts of water vapor into the atmosphere.
Over time, this water vapor condenses into clouds as liquid or frozen
droplets and is eventually followed by precipitation (rain or snow), which
returns water to the Earth’s surface. Rain eventually permeates into the
ground, where it may evaporate again if it is near the surface, flow beneath
the surface, or be stored for long periods. More easily observed is surface
runoff: the flow of fresh water either from rain or melting ice. Runoff can
then make its way through streams and lakes to the oceans or flow directly
to the oceans themselves.
Rain and surface runoff are major ways in which minerals, including
carbon, nitrogen, phosphorus, and sulfur, are cycled from land to water. The
environmental effects of runoff will be discussed later as these cycles are
described.
ne Water, Gycle
Volcanic
ste: i ns
. Zi Water in the atmosphere
7 yp Sublimation
Evapodlis piration 5
} Evaporation
\ \ C .
\ ka \ IN
Infiltragdn S43
\ \ XS
Water from the land and oceans enters the atmosphere by
evaporation or sublimation, where it condenses into clouds and
falls as rain or snow. Precipitated water may enter freshwater
bodies or infiltrate the soil. The cycle is complete when surface
or groundwater reenters the ocean. (credit: modification of
work by John M. Evans and Howard Perlman, USGS)
The Carbon Cycle
Carbon is the second most abundant element in living organisms. Carbon is
present in all organic molecules, and its role in the structure of
macromolecules is of primary importance to living organisms. Carbon
compounds contain especially high energy, particularly those derived from
fossilized organisms, mainly plants, which humans use as fuel. Since the
1800s, the number of countries using massive amounts of fossil fuels has
increased. Since the beginning of the Industrial Revolution, global demand
for the Earth’s limited fossil fuel supplies has risen; therefore, the amount of
carbon dioxide in our atmosphere has increased. This increase in carbon
dioxide has been associated with climate change and other disturbances of
the Earth’s ecosystems and is a major environmental concern worldwide.
Thus, the “carbon footprint” is based on how much carbon dioxide is
produced and how much fossil fuel countries consume.
The carbon cycle is most easily studied as two interconnected sub-cycles:
one dealing with rapid carbon exchange among living organisms and the
other dealing with the long-term cycling of carbon through geologic
processes. The entire carbon cycle is shown in [link].
he Garbon Gyele
V
Li > J
"i ~ i i irati A
Fossil ca¥bon..1 ., Microbial respiration .
[| and decomposition
Carbon dioxide gas exists in the atmosphere and is dissolved in
water. Photosynthesis converts carbon dioxide gas to organic
carbon, and respiration cycles the organic carbon back into
carbon dioxide gas. Long-term storage of organic carbon
occurs when matter from living organisms is buried deep
underground and becomes fossilized. Volcanic activity and,
more recently, human emissions, bring this stored carbon back
into the carbon cycle. (credit: modification of work by John M.
Evans and Howard Perlman, USGS)
The Biological Carbon Cycle
Living organisms are connected in many ways, even between ecosystems.
A good example of this connection is the exchange of carbon between
autotrophs and heterotrophs within and between ecosystems by way of
atmospheric carbon dioxide. Carbon dioxide is the basic building block that
most autotrophs use to build multi-carbon, high energy compounds, such as
glucose. The energy harnessed from the sun is used by these organisms to
form the covalent bonds that link carbon atoms together. These chemical
bonds thereby store this energy for later use in the process of respiration.
Most terrestrial autotrophs obtain their carbon dioxide directly from the
atmosphere, while marine autotrophs acquire it in the dissolved form
(carbonic acid, HyCO3 _). However carbon dioxide is acquired, a by-product
of the process is oxygen. Photosynthetic organisms are responsible for the
approximately 21 percent oxygen content of the atmosphere that we
observe today.
Heterotrophs and autotrophs are partners in biological carbon exchange
(especially the primary consumers, largely herbivores). Heterotrophs
acquire the high-energy carbon compounds from the autotrophs by
consuming them, and breaking them down by respiration to obtain cellular
energy, such as ATP. The most efficient type of respiration, aerobic
respiration, requires oxygen obtained from the atmosphere or dissolved in
water. Thus, there is a constant exchange of oxygen and carbon dioxide
between the autotrophs (which need the carbon) and the heterotrophs
(which need the oxygen). Gas exchange through the atmosphere and water
is one way that the carbon cycle connects all living organisms on Earth.
The Biogeochemical Carbon Cycle
The movement of carbon through the land, water, and air is complex, and in
many cases, it occurs much more slowly geologically than it does between
living organisms. Carbon is stored for long periods in what are known as
carbon reservoirs, which include the atmosphere, bodies of liquid water
(mostly oceans), ocean sediment, soil, land sediments (including fossil
fuels), and the Earth’s interior.
As stated, the atmosphere is a major reservoir of carbon in the form of
carbon dioxide and is essential to the process of photosynthesis. The level
of carbon dioxide in the atmosphere is greatly influenced by the reservoir of
carbon in the oceans. The exchange of carbon between the atmosphere and
water reservoirs influences how much carbon is found in each location, and
each one affects the other reciprocally. Carbon dioxide (CO>) from the
atmosphere dissolves in water and combines with water molecules to form
carbonic acid, and then it ionizes to carbonate and bicarbonate ions ([link])
Step 2: CO2 (dissolved) + HzO = H2CO3 (carbonic acid)
Step 4: HCO3- = H* + CO3* (carbonate ion)
Carbon dioxide reacts with water
to form bicarbonate and carbonate
ions.
The equilibrium coefficients are such that more than 90 percent of the
carbon in the ocean is found as bicarbonate ions. Some of these ions
combine with seawater calcium to form calcium carbonate (CaCO3), a
major component of marine organism shells. These organisms eventually
form sediments on the ocean floor. Over geologic time, the calcium
carbonate forms limestone, which comprises the largest carbon reservoir on
Earth.
On land, carbon is stored in soil as a result of the decomposition of living
organisms (by decomposers) or from weathering of terrestrial rock and
minerals. This carbon can be leached into the water reservoirs by surface
runoff. Deeper underground, on land and at sea, are fossil fuels: the
anaerobically decomposed remains of plants that take millions of years to
form. Fossil fuels are considered a non-renewable resource because their
use far exceeds their rate of formation. A non-renewable resource, such as
fossil fuel, is either regenerated very slowly or not at all. Another way for
carbon to enter the atmosphere is from land (including land beneath the
surface of the ocean) by the eruption of volcanoes and other geothermal
systems. Carbon sediments from the ocean floor are taken deep within the
Earth by the process of subduction: the movement of one tectonic plate
beneath another. Carbon is released as carbon dioxide when a volcano
erupts or from volcanic hydrothermal vents.
Carbon dioxide is also added to the atmosphere by the animal husbandry
practices of humans. The large numbers of land animals raised to feed the
Earth’s growing population results in increased carbon dioxide levels in the
atmosphere due to farming practices and the respiration and methane
production. This is another example of how human activity indirectly
affects biogeochemical cycles in a significant way. Although much of the
debate about the future effects of increasing atmospheric carbon on climate
change focuses on fossils fuels, scientists take natural processes, such as
volcanoes and respiration, into account as they model and predict the future
impact of this increase.
The Nitrogen Cycle
Nitrogen is an essential nutrient for living processes; it is a major
component of proteins and nucleic acids. Proteins are important biological
molecules because all cellular activities are driven by proteins. Nucleic
Acids are the building blocks of DNA (hereditary material). Nitrogen is
often the limiting nutrient (necessary for growth) on terrestrial ecosystems
[link].
Getting nitrogen into the living world is difficult. Plants and phytoplankton
are not equipped to incorporate nitrogen from the atmosphere (which exists
as tightly bonded, triple covalent Nz) even though this molecule comprises
approximately 78 percent of the atmosphere. Nitrogen enters the living
world via free-living and symbiotic bacteria, which incorporate nitrogen
into their macromolecules through nitrogen fixation (conversion of N>).
Cyanobacteria live in most aquatic ecosystems where sunlight is present;
they play a key role in nitrogen fixation. Cyanobacteria are able to use
inorganic sources of nitrogen to “fix” nitrogen. Rhizobium bacteria live
symbiotically in the root nodules of legumes (such as peas, beans, and
peanuts) and provide them with the organic nitrogen they need. Free-living
bacteria, such as Azotobacter, are also important nitrogen fixers. In
addition, humans industrially fix nitrogen to produce artificial fertilizers.
Organic nitrogen is especially important to the study of ecosystem
dynamics since many ecosystem processes, such as primary production and
decomposition, are limited by the available supply of nitrogen. As shown in
[link], the nitrogen that enters living systems by nitrogen fixation is
successively converted from organic nitrogen back into nitrogen gas by
bacteria. This process occurs in three steps in terrestrial systems:
ammonification, nitrification, and denitrification. First, the ammonification
process converts nitrogenous waste from living animals or from the remains
of dead animals into ammonium (NH,’) by certain bacteria and fungi.
Second, the ammonium is converted to nitrites (NO, _) by nitrifying
bacteria, such as Nitrosomonas, through nitrification. Subsequently, nitrites
are converted to nitrates (NO3_) by similar organisms. Third, the process of
denitrification occurs, whereby bacteria, such as Pseudomonas and
Clostridium, convert the nitrates into nitrogen gas, allowing it to re-enter
the atmosphere.
suire Nitrogen Cycle
Denitrification
by bacteria
|
Nitrification by Nitrogenous
bacteria to NO; wastes in soil
nN
y \ \ 4
| v
Ammonification Nitrogen
Nitrification by by bacteria and <__ fixation
bacteria to NOz »“Y fungi to NH,* > ' by bacteria
Nitrogen enters the living world from the atmosphere via
nitrogen-fixing bacteria. This nitrogen and nitrogenous waste
from animals is then processed back into gaseous nitrogen by
soil bacteria, which also supply terrestrial food webs with the
organic nitrogen they need. (credit: modification of work by
John M. Evans and Howard Perlman, USGS)
Human activity can release nitrogen into the environment by two primary
means: the combustion of fossil fuels, which releases different nitrogen
oxides, and by the use of artificial fertilizers in agriculture, which are then
washed into lakes, streams, and rivers by surface runoff. Atmospheric
nitrogen is associated with several effects on Earth’s ecosystems including
the production of acid rain (as nitric acid, HNO3) and greenhouse gas (as
nitrous oxide, N»O) potentially causing climate change. A major effect from
fertilizer runoff is saltwater and freshwater eutrophication, a process
whereby nutrient runoff causes the excess growth of microorganisms,
depleting dissolved oxygen levels and killing ecosystem fauna.
A similar process occurs in the marine nitrogen cycle, where the
ammonification, nitrification, and denitrification processes are performed
by marine bacteria. Some of this nitrogen falls to the ocean floor as
sediment, which can then be moved to land in geologic time by uplift of the
Earth’s surface and thereby incorporated into terrestrial rock. Although the
movement of nitrogen from rock directly into living systems has been
traditionally seen as insignificant compared with nitrogen fixed from the
atmosphere, a recent study showed that this process may indeed be
significant and should be included in any study of the global nitrogen cycle.
[footnote]
Scott L. Morford, Benjamin Z. Houlton, and Randy A. Dahlgren,
“Increased Forest Ecosystem Carbon and Nitrogen Storage from Nitrogen
Rich Bedrock,” Nature 477, no. 7362 (2011): 78-81.
The Phosphorus Cycle
Phosphorus is another essential nutrient for living processes; it is a major
component of nucleic acids, phospholipids, and, as calcium phosphate,
makes up the supportive components of our bones. Phosphorus is often the
limiting nutrient (necessary for growth) in aquatic ecosystems ([link]).
Phosphorus occurs in nature as the phosphate ion (PO,° ). In addition to
phosphate runoff as a result of human activity (mined and used to make a
artificial fertilizer), natural surface runoff occurs when it is leached from
phosphate-containing rock by weathering, thus sending phosphates into
rivers, lakes, and the ocean. This rock has its origins in the ocean.
Phosphate-containing ocean sediments form primarily from the bodies of
ocean organisms and from their excretions. However, in remote regions,
volcanic ash, aerosols, and mineral dust may also be significant phosphate
sources. This sediment then is moved to land over geologic time by the
uplifting of areas of the Earth’s surface. Phosphorus is .
Phosphorus is also reciprocally exchanged between phosphate dissolved in
the ocean and marine ecosystems. The movement of phosphate from the
ocean to the land and through the soil is extremely slow, with the average
phosphate ion having an oceanic residence time between 20,000 and
100,000 years.
In nature, phosphorus exists as the phosphate ion (PO,° ).
Weathering of rocks and volcanic activity releases phosphate
into the soil, water, and air, where it becomes available to
terrestrial food webs. Phosphate enters the oceans via surface
runoff, groundwater flow, and river flow. Phosphate dissolved
in ocean water cycles into marine food webs. Some phosphate
from the marine food webs falls to the ocean floor, where it
forms sediment. (credit: modification of work by John M.
Evans and Howard Perlman, USGS)
Excess phosphorus and nitrogen entering these ecosystems from fertilizer
runoff, and from sewage, causes excessive growth of microorganisms. This
is known as eutrophication (the enrichment of bodies of fresh water by
inorganic plant nutrients). These abundant microorganism "blooms" then
die and decay, which can increase the rate of sedimentation. But the most
important biological effect is to deplete the oxygen which is dissolved in the
water. Oxygen is critical for most aquatic organisms, and oxygen depletion
leads to the death of many of the larger organisms, such as shellfish and
finfish. This process is responsible for dead zones in lakes and at the
mouths of many major rivers ([link]).
Particulate Organic Carbon (mg/m') Population Density (persons/km’) Dead Zone Size (km’)
wn ©
unkown « .
10 20 50 100 200 $00 1,000 ' 10 100 1,000 10k 100k 0.1 § 10 100 Ik 10k
Dead zones occur when phosphorus and nitrogen from
fertilizers cause excessive growth of microorganisms, which
depletes oxygen and kills fauna. Worldwide, large dead zones
are found in coastal areas of high population density. (credit:
NASA Earth Observatory)
A dead zone is an area within a freshwater or marine ecosystem where
large areas are depleted of their normal flora and fauna; these zones can be
caused by eutrophication, oil spills, dumping of toxic chemicals, and other
human activities. The number of dead zones has been increasing for several
years, and more than 400 of these zones were present as of 2008. One of the
worst dead zones is off the coast of the United States in the Gulf of Mexico,
where fertilizer runoff from the Mississippi River basin has created a dead
zone of over 8463 square miles. Phosphate and nitrate runoff from
fertilizers also negatively affect several lake and bay ecosystems including
the Chesapeake Bay in the eastern United States.
Biogeography
Introduction
"Biology is a science of three dimensions. The first is the study of each
species across all levels of biological organization, molecule to cell to
organism to population to ecosystem. The second dimension is the diversity
of all species in the biosphere. The third dimension is the history of each
species in turn, comprising both its genetic evolution and the environmental
change that drove the evolution. Biology, by growing in all three
dimensions, is progressing toward unification and will continue to do so." -
Edward O. Wilson, in 'Systematics and the Future of Biology', Systematics
and the Origin of Species: on Ernst Mayr's 100th anniversary, Volume 102,
Issues 22-26 (2005)
Many forces influence the communities of living organisms present in
different parts of the biosphere (all of the parts of Earth inhabited by life).
The biosphere extends into the atmosphere (several kilometers above Earth)
and into the depths of the oceans. Despite its apparent vastness to an
individual human, the biosphere occupies only a minute space when
compared to the known universe. Many abiotic forces influence where life
can exist and the types of organisms found in different parts of the
biosphere. The abiotic factors influence the distribution of biomes: large
areas of land with similar climate, flora, and fauna.
Biogeography
Biogeography is the study of the geographic distribution of living things
and the abiotic factors that affect their distribution. Abiotic factors such as
temperature and rainfall vary based mainly on latitude and elevation. As
these abiotic factors change, the composition of plant and animal
communities also changes. For example, if you were to begin a journey at
the equator and walk north, you would notice gradual changes in plant
communities. At the beginning of your journey, you would see tropical wet
forests with broad-leaved evergreen trees, which are characteristic of plant
communities found near the equator. As you continued to travel north, you
would see these broad-leaved evergreen plants eventually give rise to
seasonally dry forests with scattered trees. You would also begin to notice
changes in temperature and moisture. At about 30 degrees north, these
forests would give way to deserts, which are characterized by low
precipitation.
Moving farther north, you would see that deserts are replaced by grasslands
or prairies. Eventually, grasslands are replaced by deciduous temperate
forests. These deciduous forests give way to the boreal forests found in the
subarctic, the area south of the Arctic Circle. Finally, you would reach the
Arctic tundra, which is found at the most northern latitudes. This trek north
reveals gradual changes in both climate and the types of organisms that
have adapted to environmental factors associated with ecosystems found at
different latitudes. However, different ecosystems exist at the same latitude
due in part to abiotic factors such as atmospheric jet streams, and other
ocean currents. A simplified model of the air circulation at different
latitudes, which is a primary cause of the climate and ecozones at different
latitudes, is shown in the figure below. There are six rotating cells of air in
the upper atmosphere (three north of the equator, and three south of the
equator) that, combined with the earth's rotation, create the earth's climate
and influence the distribution of plants and animals.
Global Air Circulation patterns
Tropopause
in arctic zone
Tropopause
in temperate
Polar cell
Mid-latitude cell
Hadley cell
Intertropical
convergence
zone
0°
Hadley cell
30°S
Mid-latitude cell
Polar cell
Simplified diagram of the upper air circulation patterns that help create
the earth's climate. (modified from Wikimedia Commons). Rising and
descending air creates three "cells" that encircle the globe. High
pressure areas are created in regions where the air descends; low
pressure areas arise where the air is ascending. Descending air has lost
much of its moisture (there are lots of thunderstorms in the tropics!),
and so moisture is absorbed in those regions where dryer air returns to
the surface (e.g. 30 degrees N and 30 degrees S). This results in a band
of desert regions at those latitudes.
Ecologists who study biogeography are especially interested in patterns of
species distribution. No species exists everywhere; most are found in
relatively small areas of the world. For example, the Venus flytrap is
endemic to a small area in North and South Carolina. An endemic species
is one which is naturally found only in a specific geographic area that is
usually restricted in size. Other species are generalists: species which live in
a wide variety of geographic areas; the raccoon, for example, is native to
most of North and Central America. Some birds (e.g. Osprey, Pandion
halietus) are found in appropriate habitats on several continents.
Species distribution patterns are based on biotic and abiotic factors, and are
also influenced by events occurring during the very long periods of time
required for species evolution. Early studies of biogeography were closely
linked to the emergence of evolutionary thinking in the eighteenth century,
and, in fact, observations of these patterns helped Wallace and Darwin
formulate the theory of evolution. Some of the most distinctive assemblages
of plants and animals occur in regions that have been physically separated
for millions of years by geographic barriers. Biologists estimate that
Australia, for example, has between 600,000 and 700,000 species of plants
and animals; 92% of the plant species, and 83% of the mammal species in
Australia are endemic (found on no other continent). See the Figure below
for a couple of examples. This is a consequence of the fact that Australia
and Asia have been geographically separated for at least 50 million years.
Australia is home to many endemic species. The (a)
wallaby (Wallabia bicolor), a medium-sized member
of the kangaroo family, is a pouched mammal, or
marsupial. The (b) echidna (Tachyglossus aculeatus)
is an egg-laying mammal. (credit a: modification of
work by Derrick Coetzee; credit b: modification of
work by Allan Whittome)
Sometimes ecologists discover unique patterns of species distribution by
determining where species are not found. Hawaii, for example, has no
native land species of reptiles or amphibians, and has only one native
terrestrial mammal, the hoary bat. Most of New Guinea lacks placental
mammals, and prior to human settlement, there were no land mammals in
New Zealand except for three species of bats.
Plants can be endemic or generalists: endemic plants are found only on
specific regions of the Earth, while generalists are found on many regions.
Isolated land masses—such as Australia, Hawaii, and Madagascar—often
have large numbers of endemic plant species. Some of these plants are
endangered due to human activity. The forest gardenia (Gardenia
brighamii), for instance, is endemic to Hawaii; only an estimated 15—20
trees are thought to exist ({link]).
Listed as federally
endangered, the forest
gardenia is a small tree
with distinctive flowers. It
is found only in five of the
Hawaiian Islands in small
populations consisting of a
few individual specimens.
(credit: Forest & Kim
Starr)
Energy Sources
The distribution of organisms is also influenced by the availability of
energy in their environment. Energy from the sun is captured by green
plants, algae, cyanobacteria, and photosynthetic protists. These organisms
convert solar energy into the chemical energy needed by all living things.
Light availability can be an important force directly affecting the evolution
of adaptations in photosynthesizers. For instance, plants in the understory of
a temperate forest are shaded when the trees above them in the canopy
completely leaf out in the late spring. Not surprisingly, understory plants
have adaptations to successfully capture available light. One such
adaptation is the rapid growth of spring ephemeral plants such as the spring
beauty ((link]). These spring flowers achieve much of their growth and
finish their life cycle (reproduce) early in the season before the trees in the
canopy develop leaves.
The spring beauty is an
ephemeral spring plant
that flowers early in the
spring to avoid competing
with larger forest trees for
sunlight. (credit: John
Beetham)
In aquatic ecosystems, the availability of light may be limited because
sunlight is absorbed by water, plants, suspended particles, and resident
microorganisms. Toward the bottom of a lake, pond, or ocean, there may be
a zone that light cannot reach. Photosynthesis cannot take place there and,
as aresult, a number of adaptations have evolved that enable living things
to survive in these situations. For instance, aquatic plants have
photosynthetic tissue near the surface of the water; the broad, floating
leaves of a water lily ensure that this organism gets the light it needs to
survive. In totally dark environments such as hydrothermal vents in the
deep ocean, some bacteria extract energy from inorganic chemicals using
chemosynthesis, a metabolic pathway similar to photosynthesis. You'll learn
more about those pathways in a later module.
The availability of inorganic nutrients in aquatic systems is also an
important aspect of energy or photosynthesis. Many organisms sink to the
bottom of the ocean when they die in the open water; when this occurs, the
nutrients and energy in that organism are out of circulation for some time,
unless ocean upwelling occurs. Ocean upwelling is the rising of deep
ocean waters that occurs when prevailing winds blow along surface waters
near a coastline ([link]). As the wind pushes ocean waters offshore, water
from the bottom of the ocean moves up to replace this water. As a result, the
nutrients once contained in dead organisms become available for reuse by
other living organisms.
Coastline
Ocean upwelling is an important
process that recycles nutrients
and energy in the ocean. As
wind (green arrows) pushes
offshore, it causes water from
the ocean bottom (red arrows) to
move to the surface, bringing up
nutrients from the ocean depths.
In freshwater systems, the recycling of nutrients occurs in response to air
temperature changes. The nutrients at the bottom of lakes are recycled twice
each year: in the spring and fall turnover. The spring and fall turnover is a
seasonal process that recycles nutrients and oxygen from the bottom of a
freshwater ecosystem to the top ({link]). These turnovers are caused by the
formation of a thermocline: a layer of water with a temperature that is
significantly different from that of the surrounding layers. In wintertime, the
surface of lakes found in many northern regions is frozen. However, the
water under the ice is slightly warmer, and the water at the bottom of the
lake is warmer yet at 4 °C to 5 °C (39.2 °F to 41 °F). Water is densest at 4
°C; therefore, the deepest water is also the densest. The deepest water is
oxygen poor because the decomposition of organic material at the bottom of
the lake uses up available oxygen that cannot be replaced in the winter.
There is little or no photosynthesis in that season, and any diffusion of
oxygen from the atmosphere is blocked by the surface ice layer.
Note:
Seasonal turnovers in lakes
o° 4°
79 a
ao 4°
4° 4°
Winter Spring turnover
10°
g°
70
40
Summer stratification Fall turnover
21°
The spring and fall turnovers are important
processes in freshwater lakes that act to move the
nutrients and oxygen at the bottom of deep lakes to
the top. Turnover occurs because water has a
maximum density at 4 °C. Surface water
temperature changes as the seasons progress, and
denser water sinks.
In springtime, air temperatures increase and surface ice melts. When the
temperature of the surface water begins to reach 4 °C, the water becomes
heavier and sinks to the bottom. The water at the bottom of the lake is then
displaced by the heavier surface water and, thus, rises to the top. As that
water rises to the top, the sediments and nutrients from the lake bottom are
brought along with it. During the summer months, the lake water stratifies,
or forms layers, with the warmest water at the lake surface.
As air temperatures drop in the fall, the temperature of the lake water cools
to 4 °C; therefore, this causes fall turnover as the heavy cold water sinks
and displaces the water at the bottom. The oxygen-rich water at the surface
of the lake then moves to the bottom of the lake, while the nutrients at the
bottom of the lake rise to the surface ([link]). During the winter, the oxygen
at the bottom of the lake is used by decomposers and other organisms
requiring oxygen, such as fish.
Temperature
In addition to its effects on the density of water, temperature affects the
physiology (and the biogeographic distribution) of living things.
Temperature exerts an important influence on living things because few
organisms can survive at temperatures below 0° C (32° F), due to metabolic
constraints. It is also rare for living things to survive at temperatures
exceeding 45° C (113° F). This is primarily due to temperature effects on
the proteins known as enzymes. Enzymes are typically most efficient within
a narrow and specific range of temperatures; enzyme denaturation (damage)
can occur at higher temperatures, and enzymes do not work fast enough at
lower temperatures. Therefore, organisms either must maintain an internal
temperature that keeps their enzymes functioning, or they must inhabit an
environment that will keep the body within a temperature range that
supports metabolism. Some animals have adapted to enable their bodies to
survive significant temperature fluctuations. Some Antarctic fish live at
temperatures below freezing, and hibernating Arctic ground squirrels
(Urocitellus parryii) can survive if their body temperature drops below
freezing. Similarly, some bacteria are adapted to surviving in extremely hot
environments, such as geysers, boiling mud pits or deep-ocean
hydrothermal vents. Such bacteria are examples of extremophiles:
organisms that thrive in extreme environments.
Temperature can also limit the distribution of living things. Animals in
regions with large temperature fluctuations may respond with various
adaptations, such as migration, in order to survive. Migration, the
movement from one place to another, is an adaptation found in many
animals, including many that inhabit seasonally cold climates. Migration
solves problems related to temperature, locating food, and finding a mate.
In migration, for instance, the Arctic Tern (Sterna paradisaea) makes a
40,000 km (24,000 mi) round trip flight each year between its feeding
grounds in the southern hemisphere and its breeding grounds in the Arctic.
Monarch butterflies (Danaus plexippus) live in the eastern United States in
the warmer months and migrate to Mexico and the southern United States
in the wintertime. Some species of mammals also make migratory forays.
Reindeer (Rangifer tarandus) travel about 5,000 km (3,100 mi) each year to
find food. Amphibians and reptiles are more limited in their distribution
because they lack migratory ability. Not all animals that can migrate do so:
migration carries risk and comes at a high energy cost.
Other successful adaptations allow animals to stay in place and not migrate.
Some animals hibernate or estivate to survive hostile temperatures.
Hibernation enables animals to survive cold conditions, and estivation
allows animals to survive the hostile conditions of a hot, dry climate.
Animals that hibernate or estivate enter a state known as torpor: a condition
in which their metabolic rate is significantly lowered. This enables the
animal to wait until its environment better supports its survival. Some
amphibians, such as the wood frog (Rana sylvatica), have an antifreeze-like
chemical in their cells, which prevents water in the cell from freezing and
expanding until the cell is destroyed.
Water
Water is required by all living things because it is critical for cellular
processes. Since terrestrial organisms lose water to the environment by
simple diffusion, they have evolved many adaptations to retain water.
e Plants have a number of interesting features on their leaves, such as
leaf hairs and a waxy cuticle, that serve to decrease the rate of water
loss via transpiration.
e Animals that live in very dry environments have many adaptations that
allow them to survive without water intake. Kangaroo rats, which live
in arid areas in the US and Mexico, obtain most of their water from
metabolism of the carbohydrates and lipids in the seeds that make up
their diet. They almost never drink water, and would rarely see liquid
water in their normal habitats. They also produce very small amounts
of highly concentrated, nearly crystalline, urine.
e Freshwater organisms are surrounded by water and are constantly in
danger of having water rush into their cells because of osmosis. Many
adaptations of organisms living in freshwater environments have
evolved to ensure that solute concentrations in their bodies remain
within appropriate levels. One such adaptation is the excretion of
dilute urine.
e Marine organisms are surrounded by water with a higher solute
concentration than the organism and, thus, are in danger of losing
water to the environment because of osmosis. These organisms have
morphological and physiological adaptations to retain water and
release solutes into the environment. For example, Marine Iguanas
(Amblyrhynchus cristatus), sneeze out water vapor that is high in salt
in order to maintain solute concentrations within an acceptable range
while swimming in the ocean and eating marine plants.
Inorganic Nutrients and Soil
Inorganic nutrients, such as nitrogen and phosphorus, are important in the
distribution and the abundance of living things. Plants obtain these
inorganic nutrients from the soil when water moves into the plant through
the roots. Therefore, soil structure (particle size of soil components), soil
pH, and soil nutrient content play an important role in the distribution of
plants. Animals obtain inorganic nutrients from the food they consume.
Therefore, animal distributions are related to the distribution of what they
eat. In some cases, animals will follow their food resource as it moves
through the environment.
Other Aquatic Factors
Some abiotic factors, such as oxygen, are important in aquatic ecosystems
as well as terrestrial environments. Terrestrial animals obtain oxygen from
the air they breathe. Oxygen availability can be an issue for organisms
living at very high elevations, however, where there are fewer molecules of
oxygen in the air. In aquatic systems, the concentration of dissolved oxygen
is related to water temperature and the speed at which the water moves.
Cold water has more dissolved oxygen than warmer water. In addition,
salinity, current, and tide can be important abiotic factors in aquatic
ecosystems.
Other Terrestrial Factors
Wind can be an important abiotic factor because it influences the rate of
evaporation and transpiration. The physical force of wind is also important
because it can move soil, water, or other abiotic factors, as well as an
ecosystem’s organisms.
Fire is another terrestrial factor that can be an important agent of
disturbance in terrestrial ecosystems. Some organisms are adapted to fire
and, thus, require the high heat associated with fire to complete a part of
their life cycle. For example, the jack pine—a coniferous tree—requires
heat from fire for its seed cones to open ((link]). Through the burning of
pine needles, fire adds nitrogen to the soil and limits competition by
destroying undergrowth. Closer to home, the tallgrass prairie ecosystem of
the Kansas Flint Hills is dependent on fire and grazing by large herbivores
(formerly bison, now cattle). In the absence of such disturbances, the
grasslands of the Flint Hills become scrubby cedar forests in just a few
decades.
(b)
(a) The mature cones of the jack pine (Pinus banksiana) open only
when exposed to high temperatures, such as during a forest fire. A
fire is likely to kill most vegetation, so a seedling that germinates
after a fire is more likely to receive ample sunlight than one that
germinates under normal conditions. (credit: USDA) (b) A controlled
burn moves across the Konza Prairie Biological Station. Fire is a
critical determinant in the maintenance of the tallgrass prairie
ecosystem. (photo by D.A. Rintoul)
Abiotic Factors Influencing Plant Growth
Temperature and moisture are important influences on plant production and
the amount of organic matter available to other organisms (net primary
productivity). Net primary productivity is an estimation of all of the
organic matter available to organisms in other trophic levels; it is calculated
as the total amount of carbon incorporated into plant tissues per year minus
the amount that is used during plant metabolism. In terrestrial
environments, net primary productivity is estimated by measuring the
aboveground biomass per unit area, which is the total mass of living plants,
excluding roots. This means that a large percentage of plant biomass which
exists underground is not included in this measurement. Net primary
productivity is an important variable when considering differences between
biomes. Very productive biomes have a high level of net primary
productivity, i.e., a large amount of energy at the primary producer trophic
level.
Annual biomass production is directly related to the abiotic components of
the environment. Environments with the greatest amount of biomass have
conditions in which photosynthesis, plant growth, and the resulting net
primary productivity are optimized. The climate of these areas is warm,
wet, and usually stable year-round. Photosynthesis can proceed at a high
rate, enzymes can work most efficiently, and stomata can remain open
without the risk of excessive transpiration. Together, these factors lead to
the maximal amount of carbon dioxide (CO>) moving into the plant,
resulting in high biomass production. This biomass produces several
important resources for other living things, including habitat and food.
Conversely, dry and cold environments have lower photosynthetic rates and
therefore less biomass. The animal communities, and the complexity of the
food webs, will also be affected by the decrease in available energy at the
primary producer level.
Biomes
"The sea, the woods, the mountains, all suffer in comparison with the
prairie...The prairie has a stronger hold upon the senses. Its sublimity arises
from its unbounded extent, its barren monotony and desolation, its still,
unmoved, calm, stern, almost self-confident grandeur, its strange power of
deception, its want of echo, and, in fine, its power of throwing a man back
upon himself." - Albert Pike (1831-32, Journeys in the Prairie)
Konza Prairie
A grassland Biome - Konza Prairie, near Manhattan, KS.
(photograph by David A. Rintoul)
The prairie grassland biome, described by Pike, is one of the Earth's great
biomes. But what is a biome, exactly? Biomes are large areas of land (or
water) with similar climate, flora, and fauna. The Earth’s biomes are
categorized into two major groups: terrestrial and aquatic. Terrestrial
biomes are based on land, while aquatic biomes include both ocean and
freshwater biomes. The eight major terrestrial biomes on Earth are each
distinguished by characteristic temperatures and amount of precipitation.
Comparing the annual totals of precipitation and fluctuations in
precipitation from one biome to another provides clues as to the importance
of abiotic factors in the distribution of biomes. Temperature variation on a
daily and seasonal basis is also important for predicting the geographic
distribution of the biome and the vegetation type in the biome. The
distribution of these biomes shows that the same biome can occur in
geographically distinct areas with similar climates ([link]).
Note:
Biomes
Mi Tropical forest Savanna MS Desert @ Chaparral {™ Temperate forest
{Boreal forest @ Tundra @® Mountains ) Polar ice (Temperate grassland
Each of the world’s major biomes is distinguished by
characteristic temperatures and amounts of precipitation.
Polar ice and mountains are also shown.
Rainforest
Rainforests are also referred to as tropical rainforests. This biome is found
in equatorial regions (({link]). The vegetation is characterized by plants with
broad leaves that fall off throughout the year. Unlike the trees of deciduous
forests, the trees in this biome do not have a seasonal loss of leaves
associated with variations in temperature and sunlight; these forests are
“evergreen” year-round.
The temperature and sunlight profiles of tropical rainforests are very stable
in comparison to that of other terrestrial biomes, with the temperatures
ranging from 20 °C to 34 °C (68 °F to 93 °F). When one compares the
annual temperature variation of tropical rainforests with that of other forest
biomes, the lack of seasonal temperature variation in the tropical rainforest
becomes apparent. This lack of seasonality leads to year-round plant
growth, rather than the seasonal (spring, summer, and fall) growth seen in
other biomes. In contrast to other ecosystems, tropical ecosystems do not
have long days and short days during the yearly cycle. Instead, a constant
daily amount of sunlight (11-12 hrs per day) provides more solar radiation,
thereby, a longer period of time for plant growth.
The annual rainfall in tropical rainforests ranges from 125 to 660 cm (50—
200 in) with some monthly variation. While sunlight and temperature
remain fairly consistent, annual rainfall is highly variable. Tropical
rainforests have wet months in which there can be more than 30 cm (11-12
in) of precipitation, as well as dry months in which there are fewer than 10
cm (3.5 in) of rainfall. However, the driest month of a tropical rainforest
still exceeds the annual rainfall of some other biomes, such as deserts.
Tropical rainforests have high net primary productivity because the annual
temperatures and precipitation values in these areas are ideal for plant
growth. Therefore, the extensive biomass present in the tropical rainforest
leads to plant communities with very high species diversities ({link]).
Tropical rainforests have more species of trees than any other biome; on
average between 100 and 300 species of trees are present in a single hectare
(2.5 acres) of the Amazon region of South America. One way to visualize
this is to compare the distinctive horizontal layers within the tropical
rainforest biome. On the forest floor is a sparse layer of plants and decaying
plant matter. Above that is an understory of short shrubby foliage. A layer
of trees rises above this understory and is topped by a closed upper canopy
—the uppermost overhead layer of branches and leaves. Some additional
trees emerge through this closed upper canopy. These layers provide diverse
and complex habitats for the variety of plants, fungi, animals, and other
organisms within the tropical rainforests. For instance, epiphytes are plants
that grow on other plants, which typically are not harmed. Epiphytes are
found throughout tropical rainforest biomes. Many species of animals use
the variety of plants and the complex structure of the tropical rainforests for
food and shelter. Some organisms live several meters above ground and
have adapted to this arboreal lifestyle.
Tropical rain forests, such as these
forests of Madre de Dios, Peru,
near the Amazon River, have high
species diversity. (credit:
Roosevelt Garcia)
Savannas
Savannas are grasslands with scattered trees, and they are located in Africa,
South America, and northern Australia ({link]). Savannas are hot, tropical
areas with temperatures averaging from 24 °C to 29 °C (75 °F to 84 °F) and
an annual rainfall of 10—40 cm (3.9-15.7 in). Savannas have an extensive
dry season; for this reason, forest trees do not grow as well as they do in the
tropical wet forest (or other forest biomes). As a result, within the grasses
and forbs (herbaceous flowering plants) that dominate the savanna, there
are relatively few trees ((link]). Since fire is an important source of
disturbance in this biome, plants have evolved well-developed root systems
that allow them to quickly re-sprout after a fire.
Savannas, like this one in Taita
Hills Wildlife Sanctuary in Kenya,
are dominated by grasses. (credit:
Christopher T. Cooper)
Deserts
Deserts exist between 15 ° and 30 ° north and south latitude and are
centered on the Tropics of Cancer and Capricorn ([link]). This biome is
very dry; in some years, evaporation exceeds precipitation. Subtropical hot
deserts can have daytime soil surface temperatures above 60 °C (140 °F)
and nighttime temperatures approaching 0 °C (32 °F). In cold deserts,
temperatures can be as high as 25 °C and can drop below -30 °C (-22 °F).
Deserts are characterized by low annual precipitation of fewer than 30 cm
(12 in) with little monthly variation and lack of predictability in rainfall. In
some cases, the annual rainfall can be as low as 2 cm (0.8 in) in deserts
located in central Australia (“the Outback”) and northern Africa.
The vegetation and low animal diversity of this biome is closely related to
this low and unpredictable precipitation. Very dry deserts lack perennial
vegetation that lives from one year to the next; instead, many plants are
annuals that grow quickly and reproduce when rainfall does occur, then
they die. Many other plants in these areas are characterized by having a
number of adaptations that conserve water, such as deep roots, reduced
foliage, and water-storing stems (({link]). Seed plants in the desert produce
seeds that can be in dormancy for extended periods between rains.
Adaptations in desert animals include nocturnal behavior and burrowing.
To reduce water loss,
many desert plants have
tiny leaves or no leaves at
all. The leaves of ocotillo
(Fouquieria splendens),
shown here in the Sonora
Desert near Gila Bend,
Arizona, appear only after
rainfall, and then are shed.
Temperate Grasslands
Temperate grasslands are found throughout central North America, where
they are also known as prairies; they are also in Eurasia, where they are
known as steppes ({link]). Temperate grasslands have pronounced annual
fluctuations in temperature with hot summers and cold winters. The annual
temperature variation produces specific growing seasons for plants. Plant
growth is possible when temperatures are warm enough to sustain plant
growth and when ample water is available, which occurs in the spring,
summer, and fall. During much of the winter, temperatures are low, and
water, which is stored in the form of ice, is not available for plant growth.
Annual precipitation ranges from 25 cm to 75 cm (9.8—29.5 in). Because of
relatively lower annual precipitation in temperate grasslands, there are few
trees except for those found growing along rivers or streams. The dominant
vegetation tends to consist of grasses and some prairies sustain populations
of grazing animals [link]. The vegetation is very dense and the soils are
fertile because the subsurface of the soil is packed with the roots and
rhizomes (underground stems) of these grasses. The roots and rhizomes act
to anchor plants into the ground and replenish the organic material (humus)
in the soil when they die and decay.
The American bison (Bison bison), more
commonly called the buffalo, is a grazing
mammal that once populated American
prairies in huge numbers. (photograph by
Eva Home)
Fires, mainly caused by lightning, are a natural disturbance in temperate
grasslands. When fire is suppressed in temperate grasslands, the vegetation
eventually converts to scrub and dense forests. Often, the restoration or
management of temperate grasslands requires the use of controlled burns to
suppress the growth of trees and maintain the grasses.
Deciduous Forest
Deciduous forests are the most common biome in eastern North America,
Western Europe, Eastern Asia, Chile, and New Zealand ((link]). This biome
is found throughout mid-latitude regions. Temperatures range between -30
°C and 30 °C (-22 °F to 86 °F) and drop to below freezing on an annual
basis. These temperatures mean that temperate forests have defined
growing seasons during the spring, summer, and early fall. Precipitation is
relatively constant throughout the year and ranges between 75 cm and 150
cm (29.5—59 in).
Because of the moderate annual rainfall and temperatures, deciduous trees
are the dominant plant in this biome ([link]). Deciduous trees lose their
leaves each fall and remain leafless in the winter. Thus, no photosynthesis
occurs in the deciduous trees during the dormant winter period. Each
spring, new leaves appear as the temperature increases. Because of the
dormant period, the net primary productivity of temperate forests is less
than that of tropical wet forests. In addition, temperate forests show less
diversity of tree species than tropical wet forest biomes.
Deciduous trees are the dominant
plant in the temperate forest.
(credit: Oliver Herold)
The trees of the deciduous forests leaf out and shade much of the ground;
however, this biome is more open than tropical wet forests because trees in
the temperate forests do not grow as tall as the trees in tropical wet forests.
The soils of the deciduous forests are rich in inorganic and organic
nutrients. This is due to the thick layer of leaf litter on forest floors. As this
leaf litter decays, nutrients are returned to the soil. The leaf litter also
protects soil from erosion, insulates the ground, and provides habitats for
invertebrates (such as the pill bug or roly-poly, Armadillidium vulgare) and
their predators, such as the red-backed salamander (Plethodon cinereus).
Coniferous Forest
The coniferous forest, also known as taiga or boreal forest, is found south of
the Arctic Circle and across most of Canada, Alaska, Russia, and northern
Europe ((link]). This biome has cold, dry winters and short, cool, wet
summers. The annual precipitation is from 40 cm to 100 cm (15.7—39 in)
and usually takes the form of snow. Little evaporation occurs because of the
cold temperatures.
The long and cold winters in the coniferous forest have led to the
predominance of cold-tolerant cone-bearing plants. These are evergreen
coniferous trees like pines, spruce, and fir, which retain their needle-shaped
leaves year-round. Evergreen trees can photosynthesize earlier in the spring
than deciduous trees because less energy from the sun is required to warm a
needle-like leaf than a broad leaf. This benefits evergreen trees, which grow
faster than deciduous trees in the coniferous forest. In addition, soils in
coniferous forest regions tend to be acidic with little available nitrogen.
Leaves are a nitrogen-rich structure and deciduous trees must produce a
new set of these nitrogen-rich structures each year. Therefore, coniferous
trees that retain nitrogen-rich needles may have a competitive advantage
over the broad-leafed deciduous trees.
The net primary productivity of coniferous forests is lower than that of
deciduous forests and tropical rain forests. The above ground biomass of
coniferous forests is high because these slow-growing tree species are long
lived and accumulate standing biomass over time. Plant species diversity is
less than that seen in deciduous forests and tropical rain forests. Coniferous
forests lack the pronounced elements of the layered forest structure seen in
tropical wet forests. The structure of a coniferous forest is often only a tree
layer and a ground layer ({link]). When conifer needles are dropped, they
decompose more slowly than broad leaves; therefore, fewer nutrients are
returned to the soil to fuel plant growth.
The coniferous forest (taiga) has
low lying plants and conifer trees.
(credit: L.B. Brubaker)
Arctic Tundra
The Arctic tundra lies north of the subarctic boreal forest and is located
throughout the Arctic regions of the northern hemisphere ({link]). The
average winter temperature is -34 °C (-34 °F) and the average summer
temperature is from 3 °C to 12 °C (37 °F—52 °F). Plants in the arctic tundra
have a very short growing season of approximately 10-12 weeks. However,
during this time, there are almost 24 hours of daylight and plant growth is
rapid. The annual precipitation of the Arctic tundra is very low with little
annual variation in precipitation. And, as in the boreal forests, there is little
evaporation due to the cold temperatures.
Plants in the Arctic tundra are generally low to the ground ([link]). There is
little species diversity, low net primary productivity, and low aboveground
biomass. Deeper soils of the Arctic tundra may remain in a perennially
frozen state referred to as permafrost. The permafrost makes it impossible
for roots to penetrate deep into the soil and slows the decay of organic
matter, which inhibits the release of nutrients from organic matter. During
the growing season, the ground of the Arctic tundra can be completely
covered with plants or lichens.
if
Low-growing plants such as
shrub willow dominate the
tundra landscape, shown here
in the Arctic National Wildlife
Refuge. (credit: USFWS Arctic
National Wildlife Refuge)
Aquatic Biomes
Abiotic Factors Influencing Aquatic Biomes
Introduction
"There’s nothing wrong with enjoying looking at the surface of the ocean
itself, except that when you finally see what goes on underwater, you
realize that you’ve been missing the whole point of the ocean. Staying on
the surface all the time is like going to the circus and staring at the outside
of the tent." — Dave Barry
Like terrestrial biomes, aquatic biomes are influenced by a series of abiotic
factors. The aquatic medium—water— has different physical and chemical
properties than air, however. Even if the water in a pond or other body of
water is perfectly clear (there are no suspended particles), water, on its own,
absorbs light. As one descends into a deep body of water, there will
eventually be a depth which the sunlight cannot reach. While there are some
abiotic and biotic factors in a terrestrial ecosystem that might obscure light
(like fog, dust, or insect swarms), usually these are not permanent features
of the environment. The importance of light in aquatic biomes is central to
the communities of organisms found in both freshwater and marine
ecosystems. In freshwater systems, stratification due to differences in
density is perhaps the most critical abiotic factor and is related to the energy
aspects of light. The thermal properties of water (rates of heating and
cooling) are significant to the function of marine systems and have major
impacts on global climate and weather patterns. Marine systems are also
influenced by large-scale physical water movements, such as currents; these
are less important in most freshwater lakes.
The ocean is categorized by several areas or zones ([link]). All of the
ocean’s open water is referred to as the pelagic realm. The benthic realm
extends along the ocean bottom from the shoreline to the deepest parts of
the ocean floor. Within the pelagic realm is the photic zone, which is the
portion of the ocean that light can penetrate (approximately 200 m or 650
ft). At depths greater than 200 m, light cannot penetrate; thus, this is
referred to as the aphotic zone. The majority of the ocean is aphotic and
lacks sufficient light for photosynthesis. The deepest part of the ocean, the
Challenger Deep (in the Mariana Trench, located in the western Pacific
Ocean), is about 11,000 m (about 6.8 mi) deep. To give some perspective on
the depth of this trench, the ocean is, on average, 4267 m or 14,000 ft deep.
These realms and zones are relevant to freshwater lakes as well.
Note:
Ocean Zones
Neritic Intertidal
zone zone
; Oceanic zone
1
Pelagic realm
The ocean is divided into different zones
based on water depth and distance from the
shoreline.
Marine Biomes
The ocean is the largest marine biome. It is a continuous body of salt water
that is relatively uniform in chemical composition; it is a weak solution of
mineral salts and decayed biological matter. Within the ocean, coral reefs
are a second kind of marine biome. Estuaries, coastal areas where salt water
and fresh water mix, form a third unique marine biome.
Ocean
The physical diversity of the ocean is a significant influence on plants,
animals, and other organisms. The ocean is categorized into different zones
based on how far light reaches into the water. Each zone has a distinct
group of species adapted to the biotic and abiotic conditions particular to
that zone.
The intertidal zone, which is the zone between high and low tide, is the
oceanic region that is closest to land ({link]). Generally, most people think
of this portion of the ocean as a sandy beach. In some cases, the intertidal
zone is indeed a sandy beach, but it can also be rocky or muddy. The
intertidal zone is an extremely variable environment because of tides.
Organisms are exposed to air and sunlight at low tide and are underwater
during high tide. Therefore, living things that thrive in the intertidal zone
are adapted to being dry for long periods of time. The shore of the intertidal
zone is also repeatedly struck by waves, and the organisms found there are
adapted to withstand damage from the pounding action of the waves
({link]). The exoskeletons of shoreline crustaceans (such as the shore crab,
Carcinus maenas) are tough and protect them from desiccation (drying out)
and wave damage. Another consequence of the pounding waves is that few
algae and plants establish themselves in the constantly moving rocks, sand,
or mud.
Sea urchins, mussel shells, and
starfish are often found in the
intertidal zone, shown here in
Kachemak Bay, Alaska. (credit:
NOAA)
The neritic zone ([link]) extends from the intertidal zone to depths of about
200 m (or 650 ft) at the edge of the continental shelf. Since light can
penetrate this depth, photosynthesis can occur in the neritic zone. The water
here contains silt and is well-oxygenated, low in pressure, and stable in
temperature. Phytoplankton and floating Sargassum (a type of free-floating
marine seaweed) provide a habitat for some sea life found in the neritic
zone. Zooplankton, protists, small fishes, and shrimp are found in the neritic
zone and are the base of the food chain for most of the world’s fisheries.
Beyond the neritic zone is the open ocean area known as the oceanic zone
({link]). Within the oceanic zone there is thermal stratification where warm
and cold waters mix because of ocean currents. Abundant plankton serve as
the base of the food chain for larger animals such as whales and dolphins.
Nutrients are scarce and this is a relatively less productive part of the
marine biome. When photosynthetic organisms and the protists and animals
that feed on them die, their bodies fall to the bottom of the ocean where
they remain; unlike freshwater lakes, the open ocean lacks a process for
bringing the organic nutrients back up to the surface. The majority of
organisms in the aphotic zone include sea cucumbers (phylum
Echinodermata) and other organisms that survive on the nutrients contained
in the dead bodies of organisms in the photic zone.
Beneath the pelagic zone is the benthic realm, the deepwater region beyond
the continental shelf ([link]). The bottom of the benthic realm is comprised
of sand, silt, and dead organisms. Temperature decreases, remaining above
freezing, as water depth increases. This is a nutrient-rich portion of the
ocean because of the dead organisms that fall from the upper layers of the
ocean. Because of this high level of nutrients, a diversity of fungi, sponges,
sea anemones, marine worms, Sea stars, fishes, and bacteria exist.
The deepest part of the ocean is the abyssal zone, which is at depths of 4000
m or greater. The abyssal zone ([link]) is very cold and has very high
pressure, high oxygen content, and low nutrient content. There are a variety
of invertebrates and fishes found in this zone, but the abyssal zone does not
have plants because of the lack of light. Hydrothermal vents are found
primarily in the abyssal zone; chemosynthetic bacteria utilize the hydrogen
sulfide and other minerals emitted from the vents as an energy source and
serve as the base of the food chain found in the abyssal zone.
Coral Reefs
Coral reefs are ocean ridges formed by marine invertebrates living in warm
shallow waters within the photic zone of the ocean. They are found within
30° north and south of the equator. The Great Barrier Reef is a well-known
reef system located several miles off the northeastern coast of Australia.
Other coral reef systems are fringing islands, which are directly adjacent to
land, or atolls, which are circular reef systems surrounding a former
landmass that is now underwater. The coral organisms (members of phylum
Cnidaria) are colonies of saltwater polyps that secrete a calcium carbonate
skeleton. These calcium-rich skeletons slowly accumulate, forming the
underwater reef ({link]). Corals found in shallower waters (at a depth of
approximately 60 m or about 200 ft) have a mutualistic relationship with
photosynthetic unicellular algae. The relationship provides corals with the
majority of the nutrition and the energy they require. The waters in which
these corals live are nutritionally poor and, without this mutualism, it would
not be possible for large corals to grow. Some corals living in deeper and
colder water do not have a mutualistic relationship with algae; these corals
attain energy and nutrients using stinging cells on their tentacles to capture
prey.
It is estimated that more than 4,000 fish species inhabit coral reefs. These
fishes can feed on coral, the cryptofauna (invertebrates found within the
calcium carbonate substrate of the coral reefs), or the seaweed and algae
that are associated with the coral. In addition, some fish species inhabit the
boundaries of a coral reef; these species include predators, herbivores, or
planktivores. Predators are animal species that hunt and are carnivores or
“flesh eaters.” Herbivores eat plant material, and planktivores eat plankton.
Coral reefs are formed by
the calcium carbonate
skeletons of coral
organisms, which are
marine invertebrates in
the phylum Cnidaria.
(credit: Terry Hughes)
Note:
Evolution Connection
Global Decline of Coral Reefs
It takes a long time to build a coral reef. The animals that create coral reefs
have evolved over millions of years, continuing to slowly deposit the
calcium carbonate that forms their characteristic ocean homes. Bathed in
warm tropical waters, the coral animals and their symbiotic algal partners
evolved to survive at the upper limit of ocean water temperature.
Together, climate change and human activity pose dual threats to the long-
term survival of the world’s coral reefs. As global warming due to fossil
fuel emissions raises ocean temperatures, coral reefs are suffering. The
excessive warmth causes the reefs to expel their symbiotic, food-producing
algae, resulting in a phenomenon known as bleaching. When bleaching
occurs, the reefs lose much of their characteristic color as the algae and the
coral animals die if loss of the symbiotic zooxanthellae is prolonged.
Rising levels of atmospheric carbon dioxide further threaten the corals in
other ways; as CO, dissolves in ocean waters, it lowers the pH and
increases ocean acidity. As acidity increases, it interferes with the
calcification that normally occurs as coral animals build their calcium
carbonate homes.
When a coral reef begins to die, species diversity plummets as animals lose
food and shelter. Coral reefs are also economically important tourist
destinations, so the decline of coral reefs poses a serious threat to coastal
economies.
Human population growth has damaged corals in other ways, too. As
human coastal populations increase, the runoff of sediment and agricultural
chemicals has increased, too, causing some of the once-clear tropical
waters to become cloudy. At the same time, overfishing of popular fish
species has allowed the predator species that eat corals to go unchecked.
Although a rise in global temperatures of 1—2°C (a conservative scientific
projection) in the coming decades may not seem large, it is very significant
to this biome. When change occurs rapidly, species can become extinct
before evolution leads to new adaptations. Many scientists believe that
global warming, with its rapid (in terms of evolutionary time) and
inexorable increases in temperature, is tipping the balance beyond the point
at which many of the world’s coral reefs can recover.
Estuaries: Where the Ocean Meets Fresh Water
Estuaries are biomes that occur where a source of fresh water, such as a
river, meets the ocean. Therefore, both fresh water and salt water are found
in the same vicinity; mixing results in a diluted (brackish) saltwater.
Estuaries form protected areas where many of the young offspring of
crustaceans, mollusks, and fish begin their lives. Salinity is a very important
factor that influences the organisms and the adaptations of the organisms
found in estuaries. The salinity of estuaries varies and is based on the rate of
flow of its freshwater sources. Once or twice a day, high tides bring salt
water into the estuary. Low tides occurring at the same frequency reverse
the current of salt water.
The short-term and rapid variation in salinity due to the mixing of fresh
water and salt water is a difficult physiological challenge for the plants and
animals that inhabit estuaries. Many estuarine plant species are halophytes:
plants that can tolerate salty conditions. Halophytic plants are adapted to
deal with the salinity resulting from saltwater on their roots or from sea
spray. In some halophytes, filters in the roots remove the salt from the water
that the plant absorbs. Animals, such as mussels and clams (phylum
Mollusca), have developed behavioral adaptations that expend a lot of
energy to function in this rapidly changing environment. When these
animals are exposed to low salinity, they stop feeding, close their shells, and
switch from aerobic respiration (in which they use gills) to anaerobic
respiration (a process that does not require oxygen). When high tide returns
to the estuary, the salinity and oxygen content of the water increases, and
these animals open their shells, begin feeding, and return to aerobic
respiration.
Freshwater Biomes
Freshwater biomes include lakes and ponds (standing water) as well as
rivers and streams (flowing water). They also include wetlands, which will
be discussed later. Humans rely on freshwater biomes to provide aquatic
resources for drinking water, crop irrigation, sanitation, and industry. These
various roles and human benefits are referred to as ecosystem services.
Lakes and ponds are found in terrestrial landscapes and are, therefore,
connected with abiotic and biotic factors influencing these terrestrial
biomes.
Lakes and Ponds
Lakes and ponds can range in area from a few square meters to thousands
of square kilometers. Temperature is an important abiotic factor affecting
living things found in lakes and ponds. In the summer, thermal stratification
of lakes and ponds occurs when the upper layer of water is warmed by the
sun and does not mix with deeper, cooler water. Light can penetrate within
the photic zone of the lake or pond. Phytoplankton (algae and
cyanobacteria) are found here and carry out photosynthesis, providing the
base of the food web of lakes and ponds. Zooplankton, such as rotifers and
small crustaceans, consume these phytoplankton. At the bottom of lakes
and ponds, bacteria in the aphotic zone break down dead organisms that
sink to the bottom.
Nitrogen and phosphorus are important limiting nutrients in lakes and
ponds. Because of this, they are determining factors in the amount of
phytoplankton growth in lakes and ponds. When there is a large input of
nitrogen and phosphorus (from sewage and runoff from fertilized lawns and
farms, for example), the growth of algae skyrockets, resulting in a large
accumulation of algae called an algal bloom. Algal blooms ({link]) can
become so extensive that they reduce light penetration in water. As a result,
the lake or pond becomes aphotic and photosynthetic plants cannot survive.
When the algae die and decompose, severe oxygen depletion of the water
occurs. Fishes and other organisms that require oxygen are then more likely
to die, and resulting dead zones are found across the globe. Lake Erie and
the Gulf of Mexico represent freshwater and marine habitats where
phosphorus control and storm water runoff pose significant environmental
challenges.
The uncontrolled growth of
algae in this lake has resulted in
an algal bloom. (credit: Jeremy
Nettleton)
Rivers and Streams
Rivers and streams are continuously moving bodies of water that carry large
amounts of water from the source, or headwater, to a lake or ocean. The
largest rivers include the Nile River in Africa, the Amazon River in South
America, and the Mississippi River in North America.
Abiotic features of rivers and streams vary along the length of the river or
stream. Streams begin at a point of origin referred to as source water. The
source water is usually cold, low in nutrients, and clear. The channel (the
width of the river or stream) is narrower than at any other place along the
length of the river or stream. Because of this, the current is often faster here
than at any other point of the river or stream.
The fast-moving water results in minimal silt accumulation at the bottom of
the river or stream; therefore, the water is clear. Photosynthesis here is
mostly attributed to algae that are growing on rocks; the swift current
inhibits the growth of phytoplankton. An additional input of energy can
come from leaves or other organic material that falls into the river or stream
from trees and other plants that border the water. When the leaves
decompose, the organic material and nutrients in the leaves are returned to
the water. Plants and animals have adapted to this fast-moving water. For
instance, leeches (phylum Annelida) have elongated bodies and suckers on
both ends. These suckers attach to the substrate, keeping the leech anchored
in place. Freshwater trout species (phylum Chordata) are an important
predator in these fast-moving rivers and streams.
As the river or stream flows away from the source, the width of the channel
gradually widens and the current slows. This slow-moving water, caused by
the gradient decrease and the volume increase as tributaries unite, has more
sedimentation. Phytoplankton can also be suspended in slow-moving water.
Therefore, the water will not be as clear as it is near the source. The water is
also warmer. Worms (phylum Annelida) and insects (phylum Arthropoda)
can be found burrowing into the mud. The higher order predator vertebrates
(phylum Chordata) include waterfowl, frogs, and fishes. These predators
must find food in these slow moving, sometimes murky, waters and, unlike
the trout in the waters at the source, these vertebrates may not be able to use
vision as their primary sense to find food. Instead, they are more likely to
use taste or chemical cues to find prey.
Wetlands
Wetlands are environments in which the soil is either permanently or
periodically saturated with water. Wetlands are different from lakes because
wetlands are shallow bodies of water whereas lakes vary in depth. Emergent
vegetation consists of wetland plants that are rooted in the soil but have
portions of leaves, stems, and flowers extending above the water’s surface.
There are several types of wetlands including marshes, swamps, bogs,
mudflats, and salt marshes ((link]). The three shared characteristics among
these types—what makes them wetlands—are their hydrology, hydrophytic
vegetation, and hydric soils.
Located in southern Florida,
Everglades National Park is vast
array of wetland environments,
including sawgrass marshes,
cypress swamps, and estuarine
mangrove forests. Here, a great
egret walks among cypress
trees. (credit: NPS)
Freshwater marshes and swamps are characterized by slow and steady
water flow. Bogs develop in depressions where water flow is low or
nonexistent. Bogs usually occur in areas where there is a clay bottom with
poor percolation. Percolation is the movement of water through the pores in
the soil or rocks. The water found in a bog is stagnant and oxygen depleted
because the oxygen that is used during the decomposition of organic matter
is not replaced. As the oxygen in the water is depleted, decomposition
slows. This leads to organic acids and other acids building up and lowering
the pH of the water. At a lower pH, nitrogen becomes unavailable to plants.
This creates a challenge for plants because nitrogen is an important limiting
resource. Some types of bog plants (such as sundews, pitcher plants, and
Venus flytraps) capture insects and extract the nitrogen from their bodies.
Bogs have low net primary productivity because the water found in bogs
has low levels of nitrogen and oxygen.
Population
"Anyone who believes in indefinite growth of anything physical on a
physically finite planet is either a madman or an economist." Kenneth
Boulding, economist (President Kennedy's Environmental Advisor 1966)
In biology, a population is a very specific thing. A population is all the
members of a species living within a specific area. Populations are typically
dynamic entities. They expand and contract, but, as noted above, they
cannot expand infinitely. Populations fluctuate based on a number of factors:
seasonal and yearly changes in the environment, natural disasters such as
forest fires and volcanic eruptions, competition for resources between and
within species, and the amount of habitat (where an organism lives). The
statistical study of population dynamics, demography, uses a series of
mathematical tools to investigate how populations respond to changes in
their biotic and abiotic environments. Many of these tools were originally
designed to study human populations. For example, life tables, which detail
the life expectancy of individuals within a population, were initially
developed by life insurance companies to set insurance rates. In fact, while
the term “demographics” is commonly used when discussing humans, all
living populations can be studied using this approach.
Population Size and Density
The study of any population usually begins by determining how many
individuals of a particular species exist, and how closely associated they are
with each other. Within a particular habitat, a population can be
characterized by its population size (N), the total number of individuals,
and its population density, the number of individuals within a specific area
or volume. Population size and density are the two main characteristics used
to describe and understand populations. For example, populations with more
individuals may be more stable than smaller populations based on their
genetic variability, and thus their potential to adapt to the environment.
Alternatively, a member of a population with low population density (more
spread out in the habitat), might have more difficulty finding a mate to
reproduce compared to a population of higher density. As is shown in [link],
smaller organisms tend to be more densely distributed than larger organisms.
Note:
Relationship between Population and Body Mass in Australian Mammals
Quoll
Bandicoot
Wombat
Rat-kangaroo
Potoroo
Possom species
Tree kangaroo
Wallaby
Kangaroo
Bear cuscus
Glider species
Log density (km?)
cI
rT]
a
e
K
°
a
A
fe)
x
2.0 3.0
Log mass (grams)
Australian mammals show a typical inverse
relationship between population density and
body size.
Population Research Methods
The most accurate way to determine population size is to simply count all of
the individuals within the habitat. However, this method is often not
logistically or economically feasible, especially when studying large
habitats. Thus, scientists usually study populations by sampling a
representative portion of each habitat and using these data to make
inferences about the habitat as a whole. A variety of methods can be used to
sample populations to determine their size and density. For immobile
organisms such as plants, or for very small and slow-moving organisms, a
quadrat may be used ([link]). A quadrat is a way of marking off square areas
within a habitat, either by staking out an area with sticks and string, or by
the use of a wood, plastic, or metal square placed on the ground. After
setting the quadrats, researchers then count the number of individuals that lie
within their boundaries. Multiple quadrat samples are performed throughout
the habitat at several random locations. All of these data can then be used to
estimate the population size and population density within the entire habitat.
The number and size of quadrat samples depends on the type of organisms
under study and other factors, including the density of the organism. For
example, if sampling daffodils, a 1 m* quadrat might be used whereas with
giant redwoods, which are larger and live much further apart from each
other, a larger quadrat of 400 m* might be employed. This ensures that
enough individuals of the species are counted to get an accurate sample that
correlates with the habitat, including areas not sampled.
A scientist uses a quadrat to
measure population size and
density. (credit: NPS Sonoran
Desert Network)
For mobile organisms, such as mammals, birds, or fish, a technique called
mark and recapture is often used. This method involves marking a sample
of captured animals in some way (such as tags, bands, paint, or other body
markings), and then releasing them back into the environment to allow them
to mix with the rest of the population; later, a new sample is collected,
including some individuals that are marked (recaptures) and some
individuals that are unmarked ({link]).
Mark and recapture is used to measure the population
size of mobile animals such as (a) bighorn sheep, (b) the
California condor, and (c) salmon. (credit a:
modification of work by Neal Herbert, NPS; credit b:
modification of work by Pacific Southwest Region
USFWS; credit c: modification of work by Ingrid
Taylar)
Using the ratio of marked and unmarked individuals, scientists determine
how many individuals are in the sample. From this, calculations are used to
estimate the total population size. This method assumes that the larger the
population, the lower the percentage of tagged organisms that will be
recaptured since they will have mixed with more untagged individuals. For
example, if 80 deer are captured, tagged, and released into the forest, and
later 100 deer are captured and 20 of them are already marked, we can
determine the population size (N) using the following equation:
Equation:
(number marked first catch x total number of second catch)
number marked second catch
Using our example, the population size would be estimated at 400.
Equation:
(80 x 100)
20
= 400
Therefore, there are an estimated 400 total individuals in the original
population.
There are some limitations to the mark and recapture method. Some animals
from the first catch may learn to avoid capture in the second round, thus
inflating population estimates. Alternatively, animals may preferentially be
retrapped (especially if a food reward is offered), resulting in an
underestimate of population size. Also, some species may be harmed by the
marking technique, reducing their survival. A variety of other techniques
have been developed, including the electronic tracking of animals tagged
with radio transmitters and the use of data from commercial fishing and
trapping operations to estimate the size and health of populations and
communities.
Species Distribution
In addition to measuring simple density, further information about a
population can be obtained by looking at the distribution of the individuals.
Species dispersion patterns (or distribution patterns) show the spatial
relationship between members of a population within a habitat at a particular
point in time. In other words, they show whether members of the species
live close together or far apart, and what patterns are evident when they are
spaced apart.
Individuals in a population can be more or less equally spaced apart,
dispersed randomly with no predictable pattern, or clustered in groups.
These are known as uniform, random, and clumped dispersion patterns,
respectively ({link]). Uniform dispersion is observed in plants that secrete
substances inhibiting the growth of nearby individuals (such as the release
of toxic chemicals by the sage plant Salvia leucophylla, a phenomenon
called allelopathy or plants in arid habitats that compete intensely for limited
soil water and nutrients.) and in animals like the penguin that maintain a
defined territory. An example of random dispersion occurs with dandelion
and other plants that have wind-dispersed seeds that germinate wherever
they happen to fall in a favorable environment. A clumped dispersion may
be seen in plants that drop their seeds straight to the ground, such as oak
trees, or animals that live in groups (schools of fish or herds of elephants).
Clumped dispersions may also be a function of habitat heterogeneity. Thus,
the dispersion of the individuals within a population provides more
information about how they interact with each other than does a simple
density measurement. Just as lower density species might have more
difficulty finding a mate, solitary species with a random distribution might
have a similar difficulty when compared to social species clumped together
in groups.
Uniform Random Clumped
Species may have uniform, random, or clumped distribution.
Territorial birds such as penguins tend to have uniform
distribution. Plants such as dandelions with wind-dispersed
seeds tend to be randomly distributed. Animals such as
elephants that travel in groups exhibit clumped distribution.
(credit a: modification of work by Ben Tubby; credit b:
modification of work by Rosendahl; credit c: modification of
work by Rebecca Wood)
Demography
While population size and density describe a population at one particular
point in time, scientists must use demography to study the dynamics of a
population. Demography is the statistical study of population changes over
time: birth rates, death rates, migration and life expectancies. Each of these
measures, especially birth rates, may be affected by the population
characteristics described above. For example, a large population size results
in a higher birth rate because more potentially reproductive individuals are
present. In contrast, a large population size can also result in a higher death
rate because of competition, disease, and the accumulation of waste.
Similarly, a higher population density or a clumped dispersion pattern
results in more potential reproductive encounters between individuals,
which can increase birth rate. Migration the movement of individuals into a
population (immigration) and out of a population (emigration) can
drastically influence population growth, especially the colonization of new
areas. Lastly, a female-biased sex ratio (the ratio of males to females) or age
structure (the proportion of population members at specific age ranges)
composed of many individuals of reproductive age can increase birth rates.
In addition, the demographic characteristics of a population can influence
how the population grows or declines over time. If birth and death rates are
equal, the population remains stable. However, the population size will
increase if birth rates exceed death rates; the population will decrease if birth
rates are less than death rates. Life expectancy is another important factor;
the length of time individuals remain in the population impacts local
resources, reproduction, and the overall health of the population. These
demographic characteristics are often displayed in the form of a life table.
Life Tables
Life tables provide important information about the life history of an
organism. Life tables divide the population into age groups and often sexes,
and show how long a member of that group is likely to live. They are
modeled after actuarial tables used by the insurance industry for estimating
human life expectancy. Life tables may include the probability of
individuals dying before their next birthday (i.e., their mortality rate, the
percentage of surviving individuals dying at a particular age interval, and
their life expectancy at each interval. An example of a life table is shown in
[link] from a study of Dall mountain sheep, a species native to northwestern
North America. Notice that the population is divided into age intervals
(column A). The mortality rate (per 1000), shown in column D, is based on
the number of individuals dying during the age interval (column B) divided
by the number of individuals surviving at the beginning of the interval
(Column C), multiplied by 1000.
Equation:
number of individuals dying
mortality rate = x 1000
number of individuals surviving
For example, between ages three and four, 12 individuals die out of the 776
that were remaining from the original 1000 sheep. This number is then
multiplied by 1000 to get the mortality rate per thousand.
Equation:
12
tality rate = —-~ xl ew 15.
mortality rate 776 * 000 5.0
As can be seen from the mortality rate data (column D), a high death rate
occurred when the sheep were between 6 and 12 months old, and then
increased even more from 8 to 12 years old, after which there were few
survivors. The data indicate that if a sheep in this population were to survive
to age one, it could be expected to live another 7.7 years on average, as
shown by the life expectancy numbers in column E.
Life Table of Dall Mountain Sheep!2o™«!
Data Adapted from Edward S. Deevey, Jr., “Life Tables for Natural
Populations of Animals,” The Quarterly Review of Biology 22, no. 4
(December 1947): 283-314.
Age
interval
(years)
0-0.5
0.5-1
1-2
23
3-4
4-5
5-6
Number
dying in
age
interval
out of
1000
born
54
145
12
13
12
30
46
48
69
132
187
156
90
Number
surviving
at
beginning
of age
interval
out of
1000
born
1000
946
801
789
776
764
734
688
640
571
439
252
96
Mortality
rate per
1000 alive
at
beginning
of age
interval
54.0
153.3
15.0
16.5
15.5
39.3
62.7
69.8
107.8
231.2
426.0
619.0
907.0
Life
expectancy
or mean
lifetime
remaining
to those
attaining
age
interval
7.06
12-13 3 6 500.0 i2
13-14 3 3 1000 0.7
This life table of Ovis dalli shows the number of deaths, number of survivors,
mortality rate, and life expectancy at each age interval for the Dall mountain
sheep.
Survivorship Curves
Another tool used by population ecologists is a survivorship curve, which
is a graph of the number of individuals surviving at each age interval plotted
versus time (usually with data compiled from a life table). These curves
allow us to compare the life histories of different populations ((link]).
Humans and most primates exhibit a Type I survivorship curve because a
high percentage of offspring survive their early and middle years—death
occurs predominantly in older individuals. These types of species usually
have small numbers of offspring at one time, and they give a high amount of
parental care to them to ensure their survival. Birds and perennial
herbaceous plants are examples of an intermediate of Type II survivorship
curve because the probability of death is equal for all age classes in these
organisms. Some of the animals also may have relatively few offspring and
provide significant parental care. Trees, marine invertebrates, and most
fishes exhibit a Type III survivorship curve because very few of these
organisms survive their younger years; however, those that make it to an old
age are more likely to survive for a relatively long period of time.
Organisms in this category usually have a very large number of offspring,
but once they are born, little parental care is provided. Thus these offspring
are “on their own” and vulnerable to predation, but their sheer numbers
assure the survival of enough individuals to perpetuate the species.
Survivorship Curve
Type | (humans) {
Type Ill (trees)
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Percentage of maximum life expectancy
Survivorship curves show the
distribution of individuals in
a population according to
age. Humans and most
mammals have a Type I
survivorship curve because
death primarily occurs in the
older years. Birds have a
Type II survivorship curve, as
death at any age is equally
probable. Trees have a Type
II survivorship curve
because very few survive the
younger years, but after a
certain age, individuals are
much more likely to survive.
Population Growth
"The greatest shortcoming of the human race is our inability to understand
the exponential function." - Dr. Albert A. Bartlett, Emeritus Professor of
Physics, University of Colorado
Exponential Growth
Charles Darwin, in his theory of evolution by natural selection, was greatly
influenced by the English clergyman Thomas Malthus. Malthus published a
book in 1798 stating that populations with unlimited natural resources grow
very rapidly. This accelerating pattern of increasing population size is called
exponential growth.
The best example of exponential growth is seen in bacteria. Bacteria can
undergo cell division about every hour. If 1000 bacteria are placed in a large
flask with an unlimited supply of nutrients (so the nutrients will not become
depleted), after an hour, there is one round of division, resulting in 2000
organisms—an increase of 1000. In another hour, each of the 2000
organisms will double, producing 4000, an increase of 2000 organisms.
After the third hour, there should be 8000 bacteria in the flask, an increase
of 4000 organisms. The important concept of exponential growth is that
population growth (G)—the number of organisms added in each
reproductive generation—is accelerating; that is, it is increasing at a greater
and greater rate. After 1 day and 24 of these cycles, the population would
have increased from 1000 to more than 16 billion. When the population
size, N, is plotted over time, a J-shaped growth curve is produced ([link]).
The bacteria example is not representative of the real world where resources
are limited. Furthermore, some bacteria will die during the experiment and
thus not reproduce, lowering the growth rate. Therefore, when calculating
the growth of a population, the number of deaths (D (number organisms
that die during a particular time interval) is subtracted from the number of
births (B) (number organisms that are born during that interval). This is
shown in the following formula:
Equation:
G(population growth) = B (births) - D (deaths)
Now let's examine how the average number of births and deaths relate to
population growth. The average birth and death rates based on the number
of individuals in a population is on a per capita basis. So, the per capita
birth rate (b) is the number of births during a time interval divided by the
number of individuals in the population at that time, and the per capita
death rate (d) is the number of deaths during a time interval divided by the
number of individuals in the population at that time. See the equations
below for a simple formula.
Equation:
B(number of births)
b a Dit £AVG | ee
(per capita birth rate) N (total number of individuals)
Equation:
D(number of deaths)
d iba death tate ) Seg
(per capita death rate) =— (total number of individuals)
Now returning to the simple population growth equation above, we can
convert this simple model to one in which births and deaths are expressed
on a per capita basis for a time interval. Thus, B (births) = bN (the per
capita birth rate “b” multiplied by the number of individuals “N”) and D
(deaths) =dN (the per capita death rate “d” multiplied by the number of
individuals “N”). When substituting bN for B and dN for D in simple
growth equation, we can examine the population growth rate based on per
capita birth and death rates as seen the equation below.
Equation:
G=bN — dN
The above equation can be simplified to the following.
Equation:
G=(b —d)N
Now, the difference between per capita birth rate and per capita death rates
is further simplified by substituting the term “r” (per capita growth rate).
So, the per capita growth rate (r) is equal to the per capita birth rate (b)
minus the per capita death rate (d), or r = b - d.
Equation:
G=rN
The value “r” can be positive, meaning the population is increasing in size;
or negative, meaning the population is decreasing in size; or zero, where the
population’s size is unchanging, a condition known as zero population
growth. A further refinement of the formula recognizes that different
species have inherent differences in their per capita growth rate (often
thought of as the potential for reproduction), even under ideal conditions.
Obviously, a bacterium can reproduce more rapidly and have a higher per
capita growth rate than a human. The maximal growth rate for a species is
its biotic potential.
Other factors that influence population growth (G)
When calculating per capita growth rate (r) as above, we are referring to a
closed system where individuals from other populations are not moving in
and individuals are not leaving. Immigration and emigration are two more
factors that can influence the growth of a population. Immigration is the
movement of individuals into a population which adds individuals to the
population, and emigration is the movement of individuals out of a
population which removes individuals to a population. So, the rates of
immigration and emigration are two other factors population biologists need
to consider when describing population growth (G).
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When resources are unlimited, populations exhibit
exponential growth, resulting in a J-shaped curve.
When resources are limited, populations exhibit
logistic growth. In logistic growth, population
expansion decreases as resources become scarce, and
it levels off when the carrying capacity of the
environment is reached, resulting in an S-shaped
curve.
Logistic Growth
Exponential growth is possible only when natural resources are not limited.
This occurs only infrequently and briefly in nature, such as when a
population colonizes a new habitat or is recovering from a major
disturbance. Charles Darwin recognized this fact in his description of the
“struggle for existence,” which states that individuals will compete (with
members of their own or other species) for limited resources. The
successful ones will survive to pass on their own characteristics and traits
(which we know now are transferred by genes) to the next generation at a
greater rate (natural selection). To model the reality of limited resources,
population ecologists developed the logistic growth model.
Carrying Capacity and the Logistic Model
In the real world, with its limited resources, exponential growth cannot
continue indefinitely. Exponential growth may occur in environments where
there are few individuals and plentiful resources, but when the number of
individuals gets large enough, resources will be depleted, slowing the
growth rate. Eventually, the growth rate will plateau or level off ((link]).
This population size, which represents the maximum population size that a
particular environment can support, is called the carrying capacity, or K.
The formula we use to calculate logistic growth adds the carrying capacity
as a moderating force in the growth rate. The expression “K — N” divided by
“K” is the fraction of the carrying capacity available for further growth.
Thus, the exponential growth model is restricted by this factor to generate
the logistic growth equation:
Equation:
(K — N)
Gann
7 K
Notice that when N is very small, (K-N)/K becomes close to K/K or 1, and
the right side of the equation reduces to rN, which means the population is
growing exponentially and is not influenced by carrying capacity. On the
other hand, when N is large, (K-N)/K comes close to zero, which means that
population growth will be slowed greatly or even stopped. Thus, population
growth is greatly slowed when the population size is close to the carrying
capacity. This model also allows for negative population growth, or a
population decline. This occurs when the number of individuals in the
population exceeds the carrying capacity (because the value of (K-N)/K is
negative).
A graph of this equation yields an S-shaped curve ([link]), and it is a more
realistic model of population growth than exponential growth. There are
three different sections to an S-shaped curve. Initially, growth is exponential
because there are few individuals and ample resources available. Then, as
resources begin to become limited, the growth rate decreases. Finally,
growth levels off at the carrying capacity of the environment, with little
change in population size over time.
Role of Intraspecific Competition
The logistic model assumes that every individual within a population will
have equal access to resources and, thus, an equal chance for survival. For
plants, the amount of water, sunlight, nutrients, and the space to grow are
the important resources, whereas in animals, important resources may
include food, water, shelter, nesting space, and mates.
In the real world, variation in a trait among individuals within a population
means that some individuals will be better adapted to their environment
than others. The resulting competition between population members of the
Same species for resources is termed intraspecific competition (intra- =
“within”; -specific = “species”). Intraspecific competition for resources may
not affect populations that are well below their carrying capacity—
resources are plentiful and all individuals can obtain what they need.
However, as population size increases, this competition intensifies. In
addition, the accumulation of waste products can reduce an environment’s
Carrying capacity.
Examples of Logistic Growth
Yeast, a microscopic fungus used to make bread and alcoholic beverages,
exhibits the classical S-shaped curve when grown in a test tube ([Link]a). Its
growth levels off as the population depletes the nutrients that are necessary
for its growth. However, there are variations to this idealized curve.
Examples in wild populations include sheep and harbor seals ({link]b). In
both examples, the population size exceeds the carrying capacity for short
periods of time and then falls below the carrying capacity afterwards. This
fluctuation in population size continues to occur as the population oscillates
around its carrying capacity. Still, even with this oscillation, the logistic
model is still widely supported.
Note:
ry
N
g
ES
a)
= 8
IE
s
°
[=
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3
g
288 8 8
1980 1990 1995 2000
(b)
(a) Yeast grown in ideal conditions in a test tube show a
classical S-shaped logistic growth curve, whereas (b) a
natural population of seals shows real-world fluctuation.
Population Regulation
"If we don't halt population growth with justice and compassion, it will be
done for us by nature, brutally and without pity- and will leave a ravaged
world." - Dr. Henry W. Kendall, Nobel Laureate in Physics, 1990
The natural mechanisms regulating population growth can indeed be brutal.
Carrying capacity is a mathematical sanitization of the realities of famine,
disease, and other causes of death. And the logistic model of population
growth, while valid in many natural populations and a useful model, is a
simplification of real-world population dynamics. Implicit in the model is
that the carrying capacity of the environment does not change, which is not
the case. The carrying capacity varies annually: for example, some
summers are hot and dry whereas others are cold and wet. In many areas,
the carrying capacity during the winter is much lower than it is during the
summer. Also, natural events such as earthquakes, volcanoes, and fires can
alter an environment and hence its carrying capacity. Additionally,
populations do not usually exist in isolation. They engage in interspecific
competition: that is, they share the environment with other species,
competing with them for the same resources. These factors are also
important to understanding how a specific population will grow.
Nature regulates population growth in a variety of ways. These are grouped
into density-dependent factors, in which the density of the population at a
given time affects growth rate and mortality, and density-independent
factors, which influence mortality in a population regardless of population
density. Note that in the former, the effect of the factor on the population
depends on the density of the population at onset. Conservation biologists
want to understand both types because this helps them manage populations
and prevent extinction or overpopulation.
Density-dependent Regulation
Most density-dependent factors are biological in nature (biotic), and include
predation, inter- and intraspecific competition, accumulation of waste, and
diseases such as those caused by parasites. Usually, the denser a population
is, the greater its mortality rate. For example, during intra- and interspecific
competition, the reproductive rates of the individuals will usually be lower
and mortality rates higher, reducing their population’s rate of growth. In
addition, low prey density increases the mortality of its predator because it
has more difficulty locating its food source.
An example of density-dependent regulation is shown in [link] with results
from a study focusing on the giant intestinal roundworm (Ascaris
lumbricoides), a parasite of humans and other mammals.!{2™te] Denser
populations of the parasite exhibited lower fecundity: they contained fewer
eggs. One possible explanation for this is that females would be smaller in
more dense populations (due to limited resources) and that smaller females
would have fewer eggs. This hypothesis was tested and disproved in a 2009
study which showed that female weight had no influence. !{2o™2te! The actual
cause of the density-dependence of fecundity in this organism is still
unclear and awaiting further investigation.
N.A. Croll et al., “The Population Biology and Control of Ascaris
lumbricoides in a Rural Community in Iran.” Transactions of the Royal
Society of Tropical Medicine and Hygiene 76, no. 2 (1982): 187-197,
doi:10.1016/0035-9203(82)90272-3.
Martin Walker et al., “Density-Dependent Effects on the Weight of Female
Ascaris lumbricoides Infections of Humans and its Impact on Patterns of
Egg Production.” Parasites & Vectors 2, no. 11 (February 2009),
doi:10.1186/1756-3305-2-11.
Fecundity as a Function of Population
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Number of worms
In this population of roundworms,
fecundity (number of eggs)
decreases with population density.
[footnote]
N.A. Croll et al., “The Population
Biology and Control of Ascaris
lumbricoides in a Rural
Community in Iran.” Transactions
of the Royal Society of Tropical
Medicine and Hygiene 76, no. 2
(1982): 187-197,
doi:10.1016/0035-9203(82)90272-
2:
Density-independent Regulation and Interaction with Density-
dependent Factors
Many factors, typically physical or chemical in nature (abiotic), influence
the mortality of a population regardless of its density, including weather,
natural disasters, and pollution. An individual deer may be killed in a forest
fire regardless of how many deer happen to be in that area. Its chances of
survival are the same whether the population density is high or low. The
same holds true for cold winter weather.
In real-life situations, population regulation is very complicated and
density-dependent and independent factors can interact. A dense population
that is reduced in a density-independent manner by some environmental
factor(s) will be able to recover differently than a sparse population. For
example, a population of deer affected by a harsh winter will recover faster
if there are more deer remaining to reproduce.
Note:
Evolution Connection
Why Did the Woolly Mammoth Go Extinct?
The three photos include: (a) 1916 mural of a mammoth
herd from the American Museum of Natural History, (b)
the only stuffed mammoth in the world, from the
Museum of Zoology located in St. Petersburg, Russia,
and (c) a one-month-old baby mammoth, named Lyuba,
discovered in Siberia in 2007. (credit a: modification of
work by Charles R. Knight; credit b: modification of
work by “Tanapon”/Flickr; credit c: modification of
work by Matt Howry)
It's easy to get lost in the discussion of dinosaurs and theories about why
they went extinct 65 million years ago. Was it due to a meteor slamming
into Earth near the coast of modern-day Mexico, or was it from some long-
term weather cycle that is not yet understood? One hypothesis that will
never be proposed is that humans had something to do with it. Mammals
were small, insignificant creatures of the forest 65 million years ago, and
no humans existed.
Woolly mammoths, however, began to go extinct about 10,000 years ago,
when they shared the Earth with humans who were no different
anatomically than humans today ([link]). Mammoths survived in isolated
island populations as recently as 1700 BC. We know a lot about these
animals from carcasses found frozen in the ice of Siberia and other regions
of the north. Scientists have sequenced at least 50 percent of its genome
and believe mammoths are between 98 and 99 percent identical to modern
elephants.
It is commonly thought that climate change and human hunting led to their
extinction. A 2008 study estimated that climate change reduced the
mammoth’s range from 3,000,000 square miles 42,000 years ago to
310,000 square miles 6,000 years ago. f20™motel Tt is also well documented
that humans hunted these animals. A 2012 study showed that no single
factor was exclusively responsible for the extinction of these magnificent
creatures, |!0otmote] Ty addition to human hunting, climate change, and
reduction of habitat, these scientists demonstrated another important factor
in the mammoth’s extinction was the migration of humans across the
Bering Strait to North America during the last ice age 20,000 years ago.
David Nogués-Bravo et al., “Climate Change, Humans, and the Extinction
of the Woolly Mammoth.” PLoS Biol 6 (April 2008): e79,
doi:10.1371/journal.pbio.0060079.
G.M. MacDonald et al., “Pattern of Extinction of the Woolly Mammoth in
Beringia.” Nature Communications 3, no. 893 (June 2012),
doi:10.1038/ncomms1881.
The maintenance of stable populations was and is very complex, with
many interacting factors determining the outcome. It is important to
remember that humans are also part of nature. Once we contributed to a
species’ decline using primitive hunting technology only.
Human Population Growth
"Unlike plagues of the dark ages or contemporary diseases we do not
understand, the moder plague of overpopulation is soluble by means we
have discovered and with resources we possess. What is lacking is not
sufficient knowledge of the solution but universal consciousness of the
gravity of the problem and education of the billions who are its victim." -
Martin Luther King, Jr., civil rights leader and Nobel laureate
Concepts of animal population dynamics can be applied to human
population growth. Humans are not unique in their ability to alter their
environment. For example, beaver dams alter the stream environment where
they are built. Humans, however, have the ability to alter their environment
to increase its carrying capacity sometimes to the detriment of other species
(e.g., via artificial selection for crops that have a higher yield). Earth’s
human population is growing rapidly, to the extent that some worry about
the ability of the earth’s environment to sustain this population, as long-
term exponential growth carries the potential risks of famine, disease, and
large-scale death.
Although humans have increased the carrying capacity of their
environment, the technologies used to achieve this transformation have
caused unprecedented changes to Earth’s environment, altering ecosystems
to the point where some may be in danger of collapse. The depletion of the
ozone layer, erosion due to acid rain, and damage from global climate
change are caused by human activities. The ultimate effect of these changes
on our carrying capacity is unknown. As some point out, it is likely that the
negative effects of increasing carrying capacity will outweigh the positive
ones—the carrying capacity of the world for human beings might actually
decrease.
The world’s human population is currently experiencing exponential growth
even though human reproduction is far below its biotic potential ((link]). To
reach its biotic potential, all females would have to become pregnant every
nine months or so during their reproductive years. Also, resources would
have to be such that the environment would support such growth. Neither of
these two conditions exists. In spite of this fact, human population is still
growing exponentially.
=— World
=— Africa
~~ Asia
~~ Europe
3,000,000 == Latin America
= Northern America
5,000,000
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Human population growth since 1000 AD is
exponential (dark blue line). Notice that while
the population in Asia (yellow line), which has
many economically underdeveloped countries,
is increasing exponentially, the population in
Europe (light blue line), where most of the
countries are economically developed, is
growing much more slowly.
A consequence of exponential human population growth is the time that it
takes to add a particular number of humans to the Earth is becoming
shorter. [link] shows that 130 years were necessary to add 1 billion humans
in 1930, but it only took 24 years to add two billion people between 1975
and 1999. As already discussed, at some point it would appear that our
ability to increase our carrying capacity indefinitely on a finite world is
uncertain. Without new technological advances, the human growth rate has
been predicted to slow in the coming decades. However, the population will
still be increasing and the threat of overpopulation remains.
Time between Billions in World Population Growth
1 billion: 1800
2 billion: 1930
3 billion: 1960
4 billion: 1975
5 billion: 1987
6 billion: 1999
7 billion: 2012
8 billion: 2028
9 billion: 2054
Years
Source: Population Reference Bureau
The time between the addition of each billion human
beings to Earth decreases over time. (credit:
modification of work by Ryan T. Cragun)
Overcoming Density-Dependent Regulation
Humans are unique in their ability to alter their environment with the
conscious purpose of increasing its carrying capacity. This ability is a major
factor responsible for human population growth and a way of overcoming
density-dependent growth regulation. Much of this ability is related to
human intelligence, society, and communication. Humans can construct
shelter to protect them from the elements and have developed agriculture
and domesticated animals to increase their food supplies. In addition,
humans use language to communicate this technology to new generations,
allowing them to improve upon previous accomplishments.
Other factors in human population growth are migration and public health.
Humans originated in Africa, but have since migrated to nearly all
inhabitable land on the Earth. Public health, sanitation, and the use of
antibiotics and vaccines have decreased the ability of infectious disease to
limit human population growth. In the past, diseases such as the bubonic
plaque of the fourteenth century killed between 30 and 60 percent of
Europe’s population and reduced the overall world population by as many
as 100 million people. Today, the threat of infectious disease, while not
gone, is certainly less severe. According to the World Health Organization,
global death from infectious disease declined from 16.4 million in 1993 to
14.7 million in 1992. To compare to some of the epidemics of the past, the
percentage of the world's population killed between 1993 and 2002
decreased from 0.30 percent of the world's population to 0.24 percent. Thus,
it appears that the influence of infectious disease on human population
growth is becoming less significant.
Age Structure, Population Growth, and Economic
Development
The age structure of a population is an important factor in population
dynamics. Age structure is the proportion of a population at different age
ranges. Age structure allows better prediction of population growth, plus
the ability to associate this growth with the level of economic development
in the region. Countries with rapid growth have a pyramidal shape in their
age structure diagrams, showing a preponderance of younger individuals,
many of whom are of reproductive age or will be soon ((link]). This pattern
is most often observed in underdeveloped countries where individuals do
not live to old age because of less-than-optimal living conditions. Age
structures of areas with slow growth, including developed countries such as
the United States, have a parabola shape structure (stage 3) ([link]), with
many fewer young and reproductive-aged individuals and a greater
proportion of older individuals. Other developed countries, such as Italy,
have zero population growth. The age structure of these populations is more
conical, with an even greater percentage of middle-aged and older
individuals. The actual growth rates in different countries are shown in
[link], with the highest rates tending to be in the less economically
developed countries of Africa and Asia. Lastly, both fertility rates and age
structure interact to influence population growth rates. High fertility rates
can increase population growth because more offspring are produced per
individual, whereas a pyramid-like age structure increases growth rates
because more individuals in the population are producing offspring.
Age Structure Diagrams
Stage 1: Rapid growth Stage 2: Slow growth Stage 3: Stable Stage 4: ?
Typical age structure diagrams are shown. The rapid
growth diagram narrows to a point, indicating that the
number of individuals decreases rapidly with age. In the
slow growth model, the number of individuals decreases
steadily with age. Stable population diagrams are
rounded on the top, showing that the number of
individuals per age group decreases gradually, and then
increases for the older part of the population.
Age structure diagrams for rapidly growing, slow growing and stable
populations are shown in stages 1 through 3. What type of population
change do you think stage 4 represents? If you guessed decreasing, you are
correct.
Percent Growth in Population
M-0% —0%-1% 1% Ff 2% [] 3%+
The percent growth rate of population in different countries is
shown. Notice that the highest growth is occurring in less
economically developed countries in Africa and Asia.
Long-Term Consequences of Exponential Human Population
Growth
Many dire predictions have been made about the world’s population leading
to a major crisis called the “population explosion.” In the 1968 book The
Population Bomb, biologist Dr. Paul R. Ehrlich wrote, “The battle to feed
all of humanity is over. In the 1970s hundreds of millions of people will
starve to death in spite of any crash programs embarked upon now. At this
late date nothing can prevent a substantial increase in the world death
rate.” oolnote] While many critics view this statement as an exaggeration, the
laws of exponential population growth are still in effect, and unchecked
human population growth cannot continue indefinitely.
Paul R. Erlich, prologue to The Population Bomb, (1968; repr., New York:
Ballantine, 1970).
Efforts to control population growth led to the one-child policy in China,
which used to include severe penalties for having more than 1 child. The
policy itself, its social impacts, and the effectiveness of limiting overall
population growth are controversial. In 2016, the Chinese government
abolished the policy citing issues with age demography and sex ratios. In
spite of population control policies, the human population continues to
grow. At some point the food supply may run out because of the subsequent
need to produce more and more food to feed our population. The United
Nations estimates that future world population growth may vary from 6
billion (a decrease) to 16 billion people by the year 2100. There is no way
to know whether human population growth will moderate to the point
where the crisis described by Dr. Ehrlich will be averted.
Another result of population growth is the endangerment of the natural
environment. Many countries have attempted to reduce the human impact
on climate change by reducing their emission of the greenhouse gas carbon
dioxide. However, these treaties have not been ratified by every country,
and many underdeveloped countries trying to improve their economic
condition may be less likely to agree with such provisions if it means
slower economic development. Furthermore, the role of human activity in
causing climate change has become a hotly debated socio-political issue in
some developed countries, including the United States. Thus, we enter the
future with considerable uncertainty about our ability to curb human
population growth and protect our environment.
Community Ecology
"The outstanding scientific discovery of the twentieth century is not
television, or radio, but rather the complexity of the land organism. Only
those who know the most about it can appreciate how little we know about
it. The last word in ignorance is the man who says of an animal or plant:
"What good is it?" If the land mechanism as a whole is good, then every
part is good, whether we understand it or not." - Aldo Leopold, A Sand
County Almanac
Populations rarely, if ever, live in isolation from populations of other
species. In most cases, numerous species share a habitat. The interactions
between these populations play a major role in regulating population
growth and abundance. All populations occupying the same habitat form a
community: all populations inhabiting a specific area at the same time. The
number of species occupying the same habitat and their relative abundance
is known as species diversity. Areas with low diversity, such as the glaciers
of Antarctica, still contain a wide variety of living things, whereas the
diversity of tropical rainforests is so great that it cannot be counted.
Ecology is studied at the community level to understand how species
interact with each other and what processes determine the patterns of
species coexistence, diversity, and distributions that we see in nature Any
interactions between two or more species is referred to globally as
interspecific interactions , and there are specific terms for some of unique
interactions that will be discussed throughout this section. These unique
interactions can have a positive effect (+), a negative effect (-) or a neutral
effect (0) for the individual of the species.
Niche
In a community, no two species can have exactly the same ecological
requirement and persist together in equilibrium. In order for a species to
survive in an area, to obtain nutrients and energy and to avoid predators, a
certain combination of ecological variables are necessary. These ecological
variables include the resources available (light, nutrients, food and habitat),
environmental characteristics (temperature and water availability) and the
interactions with other organisms. These ecological requirements and
interactions are used to define an organisms niche. For example, the Black-
tailed Prairie Dog (Cynomys ludovicianus ) [link] is mostly found in short
grass prairie. They can live within a broad range of temperature and
moisture, specific soil types, and forage on specific species of grasses.
These characteristics, other variables and interspecific interactions define
their niche.
Black-Tailed Prairie Dog
The Black-tailed Prairie Dog has a
unique niche. They eat grass and
are eaten by coyotes, black-footed
ferrets and other carnivores. The
prairie dog lives in burrows and
this activity produces bare soil
areas where seeds can germinate
without being shaded by trees. The
burrows once abandoned provide
nesting sites for burrowing owls.
(photo by D. A. Rintoul)
Predation and Herbivory
Perhaps the classical example of species interaction is predation: the
hunting of prey by its predator where the predator is positively affected (+)
and the prey is negatively affected (-). Nature shows on television highlight
the drama of one living organism killing another. Populations of predators
and prey in a community are not constant over time: in most cases, they
vary in cycles that appear to be related. The most often cited example of
predator-prey dynamics is seen in the cycling of the lynx (predator) and the
snowshoe hare (prey), using nearly 200 year-old trapping data from North
American forests ([link]). This cycle of predator and prey repeats itself
approximately every 10 years, with the predator population lagging 1—2
years behind that of the prey population. As the hare numbers increase,
there is more food available for the lynx, allowing the lynx population to
increase as well. When the lynx population grows to a threshold level,
however, they kill so many hares that hare population begins to decline,
followed by a decline in the lynx population because of scarcity of food.
When the lynx population is low, the hare population size begins to increase
due, at least in part, to low predation pressure, starting the cycle anew.
Predator-prey Dynamics
[Hare (red)
|_| Lynx (blue)
Thousands of animals
1845 1865 1885 1905 1925
Time (years)
The cycling of lynx and snowshoe hare
populations in Northern Ontario is an example
of predator-prey dynamics.
The idea that the population cycling of the two species is entirely controlled
by predation models has come under question. More recent studies have
pointed to undefined density-dependent factors as being important in the
cycling, in addition to predation. One possibility is that the cycling is
inherent in the hare population due to density-dependent effects such as
lower fecundity (maternal stress) caused by crowding when the hare
population gets too dense. The hare cycling would then induce the cycling
of the lynx because it is the lynxes’ major food source. In addition, many
populations of annual plants show periodic cycles that are completely
unrelated to any predator or herbivore population. The more we study
communities, the more complexities we find, allowing ecologists to derive
more accurate and sophisticated models of population dynamics.
Herbivory describes the consumption of plants by insects and other animals,
and it is another interspecific relationship that affects populations. Unlike
animals, most plants cannot outrun predators or use mimicry to hide from
hungry animals. Some plants have developed mechanisms to defend against
herbivory. Other species have developed mutualistic relationships; for
example, herbivory provides a mechanism of seed distribution that aids in
plant reproduction.
Defense Mechanisms against Predation and Herbivory
The study of communities must consider evolutionary forces that act on the
members of the various populations contained within it. Species are not
static, but slowly changing and adapting to their environment by natural
selection and other evolutionary forces. Species have evolved numerous
mechanisms to escape predation and herbivory. These defenses may be
mechanical, chemical, physical, or behavioral.
Mechanical defenses, such as the presence of thorns on plants or the hard
shell on turtles, discourage animal predation and herbivory by causing
physical pain to the predator or by physically preventing the predator from
being able to eat the prey. Chemical defenses are produced by many
animals as well as plants, such as the foxglove which is extremely toxic
when eaten. [link] shows some organisms’ defenses against predation and
herbivory.
(d)
(c)
The (a) honey locust tree (Gleditsia triacanthos) uses
thorns, a mechanical defense, against herbivores,
while the (b) Florida red-bellied turtle (Pseudemys
nelsoni) uses its shell as a mechanical defense against
predators. (c) Foxglove (Digitalis sp.) uses a chemical
defense: toxins produced by the plant can cause
nausea, vomiting, hallucinations, convulsions, or death
when consumed. (d) The North American millipede
(Narceus americanus) uses both mechanical and
chemical defenses: when threatened, the millipede
curls into a defensive ball and produces a noxious
substance that irritates eyes and skin. (credit a:
modification of work by Huw Williams; credit b:
modification of work by “JamieS93”/Flickr; credit c:
modification of work by Philip Jagenstedt; credit d:
modification of work by Cory Zanker)
Many species use their body shape and coloration to avoid being detected
by predators. The crab spider has the coloration and body shape of a flower
petal which makes it very hard to see when stationary against a background
of real a real flower ([link]a). In another example, the chameleon can
change its color to match its surroundings ([link]b). Both of these are
examples of camouflage, or avoiding detection by blending in with the
background.
(a) The crab spider (a) and the chameleon (b) use
body shape and/or coloration to deceive potential
prey, and to prevent detection by predators. (credit a:
photograph by David A. Rintoul; credit b:
modification of work by Frank Vassen)
Some species use coloration as a way of warning predators that they are not
good to eat. For example, the cinnabar moth caterpillar, the fire-bellied
toad, and many species of beetle have bright colors that warn of a foul taste,
the presence of toxic chemical, and/or the ability to sting or bite,
respectively. Predators that ignore this coloration and eat the organisms will
experience their unpleasant taste or presence of toxic chemicals and learn
not to eat them in the future. This type of defensive mechanism is called
aposematic coloration, or warning coloration ((link]).
St)
(a) (b)
(a) The strawberry poison dart frog (Oophaga
pumilio) uses aposematic coloration to warn predators
that it is toxic, while the (b) striped skunk (Mephitis
mephitis) uses aposematic coloration to warn predators
of the unpleasant odor it produces. (credit a:
modification of work by Jay Iwasaki; credit b:
modification of work by Dan Dzurisin)
While some predators learn to avoid eating certain potential prey because of
their coloration, other species have evolved mechanisms to mimic this
coloration to avoid being eaten, even though they themselves may not be
unpleasant to eat or contain toxic chemicals. In Batesian mimicry, a
harmless species imitates the warning coloration of a harmful one.
Assuming they share the same predators, this coloration then protects the
harmless ones, even though they do not have the same level of physical or
chemical defenses against predation as the organism they mimic. Many
insect species mimic the coloration of wasps or bees, which are stinging,
venomous insects, thereby discouraging predation ((link]).
Batesian mimicry occurs when a harmless species
mimics the coloration of a harmful species, as is seen
with the (a) bumblebee and (b) bee-like robber fly.
(credit a, b: modification of work by Cory Zanker)
In Miillerian mimicry, multiple species share the same warning coloration,
but all of them actually have defenses. [link] shows a variety of foul-tasting
butterflies with similar coloration.
Several unpleasant-tasting Heliconius
butterfly species share a similar color
pattern, an example of Miillerian mimicry.
(credit: Joron M, Papa R, Beltran M,
Chamberlain N, Mavarez J, et al.)
Competition
Resources are often limited within a habitat and multiple species may
compete to obtain them. All species have an ecological niche in the
ecosystem, which describes how they acquire the resources they need and
how they interact with other species in the community. So, the plants in a
garden are competing with each other for soil nutrients, and water. This
competition between the different species is called interspecific
competition. The overall effect on both species is negative because either
one of the species would do better if the other species is not present. So,
how do species reduce the overall negative effects of direct competition?
Competitive Exclusion Principle
The competitive exclusion principle states that two species cannot occupy
the same niche in a habitat and stably coexist. In other words, different
species cannot coexist in a community if they are competing for all the
same resources. An example of this principle is shown in [link], with two
protozoan species, Paramecium aurelia and Paramecium caudatum. When
grown individually in the laboratory, they both thrive. But when they are
placed together in the same test tube (habitat), P. aurelia outcompetes P.
caudatum for food, leading to the latter’s eventual extinction.
P. aurelia alone P. caudatum alone
Number of cells
rF FPN
10 10
Time (days) Time (days)
Both species grown together
NO N
S isa}
o oO
ee
an
Number of cells
10
Time (days)
Paramecium aurelia and Paramecium caudatum grow well
individually, but when they compete for the same resources,
the P. aurelia outcompetes the P. caudatum.
Resource partitioning
This exclusion may be avoided if a population evolves to make use of a
different resource, a different area of the habitat, or feeds during a different
time of day, called resource partitioning. The two organisms are then said to
occupy different niches. These organisms coexist by minimizing direct
competition. The anole lizards found on a single island are a good example
of resource partitioning [link] because it shows the effects of how natural
selection has driven the evolution of different species in order to reduce
competition.
; - incensis
This figure shows resource partitioning among 11
species of anole lizards found on the island of Puerto
Rico. Each species occupies a different type or elevation
of vegetation. The habitat is further partitioned by the
amount of sunlight and moisture available. Image by Eva
Horne modified from (Williams, E.E. 1983. Ecomorphs,
faunas, island size, and diverse end points in island
radiations of Anolis. In Lizard Ecology: Studies of a
Model Organism. Eds. R.B. Huey, E.R. Pianka, and T.W.
Schoener. Harvard University Press).
Symbiosis
Symbiotic relationships, or symbioses (plural), are close interactions
between individuals of different species over an extended period of time
that impact the abundance and distribution of the associating populations.
Symbiosis is a greek word meaning “living together”. At least one of the
species is dependent upon the other (they are not free-living), and often
both species are dependent. Most scientists accept this definition, but some
restrict the term to only those species that are mutualistic, where both
individuals benefit from the interaction. In this discussion, the first broader
definition will be used.
Commensalism
A commensal relationship occurs when one species benefits (+) from the
close, prolonged interaction, while the other neither benefits nor is harmed
(0). Birds nesting in trees provide an example of a commensal relationship
({link]). The tree is not harmed by the presence of the nest among its
branches. The nests are light and produce little strain on the structural
integrity of the branch, and most of the leaves, which the tree uses to get
energy by photosynthesis, are above the nest so they are unaffected. The
bird, on the other hand, benefits greatly. If the bird had to nest in the open,
its eggs and young would be vulnerable to predators. Another example of a
commensal relationship is the clown fish and the sea anemone. The sea
anemone is not harmed by the fish, and the fish gains protection from
predators who would be stung upon nearing the sea anemone.
The southern masked-weaver
bird is starting to make a nest
in a tree in Zambezi Valley,
Zambia. This is an example
of a commensal relationship,
in which one species (the
bird) benefits, while the other
(the tree) neither benefits nor
is harmed. (credit:
“Hanay”/Wikimedia
Commons)
Mutualism
A second type of species interaction is called mutualism, where two
species benefit from their interaction (+,+). For example, termites have a
mutualistic relationship with protozoa that live in the insect’s gut ([link]a).
The termite benefits from the ability of bacterial symbionts within the
protozoa to digest cellulose. The termite itself cannot do this, and without
the protozoa, it would not be able to obtain energy from its food (cellulose
from the wood it chews and eats). The protozoa and the bacterial symbionts
benefit by having a protective environment and a constant supply of food
from the wood chewing actions of the termite. Lichens have a mutualistic
relationship between fungus and photosynthetic algae or bacteria ({link]b).
As these symbionts grow together, the glucose produced by the algae
provides nourishment for both organisms, whereas the physical structure of
the lichen protects the algae from the elements and makes certain nutrients
in the atmosphere more available to the algae. Another example of
mutualism is the interaction between a plant and its insect pollinator. The
plant benefits from having its pollen transferred to another individual to
carry out reproduction and the insect benefits from nectar or other reward
provided by the plant. This is an example of a non-symbiotic mutualism as
both the plant and the insect are free-living organisms.
(a) Termites form a mutualistic relationship with
symbiotic protozoa in their guts, which allow both
organisms to obtain energy from the cellulose the
termite consumes. (b) Lichen is a fungus that has
symbiotic photosynthetic algae living inside its cells.
(credit a: modification of work by Scott Bauer,
USDA; credit b: modification of work by Cory
Zanker)
Parasitism
A parasite is an organism that lives in or on another living organism and
derives nutrients from it. In this relationship, the parasite benefits (+), but
the organism being fed upon, the host is harmed (-). The host is usually
weakened by the parasite as it siphons resources the host would normally
use to maintain itself. The parasite, however, is unlikely to kill the host,
especially not quickly, because this would allow no time for the organism to
complete its reproductive cycle by spreading to another host.
The reproductive cycles of parasites are often very complex, sometimes
requiring more than one host species. A tapeworm is a parasite that causes
disease in humans when contaminated, undercooked meat such as pork,
fish, or beef is consumed ([link]). The tapeworm can live inside the
intestine of the host for several years, benefiting from the food the host is
bringing into its gut by eating, and may grow to be over 50 ft long by
adding segments. The parasite moves from species to species in a cycle,
making two hosts necessary to complete its life cycle. Another common
parasite is Plasmodium falciparum, the protozoan cause of malaria, a
significant disease in many parts of the world. Living in human liver and
red blood cells, the organism reproduces asexually in the gut of blood-
feeding mosquitoes to complete its life cycle. Thus malaria is spread from
human to human by mosquitoes, one of many arthropod-borne infectious
diseases.
Tapeworm (Taenia) Infection
Embryos develop into
larvae in muscles of Cysts may develop
3) Tapeworm embryos pigs or humans. in any organ, and are most
hatch, penetrate the common in subcutaneous
intestinal wall, a A tissue as well as in the
and circulate brain and eyes.
to musculature
in pigs or humans. Humans acquire the
< infection by ingesting @}
raw or undercooked
meat from an infected
animal host.
O
2 a/ 5)
U The tapeworm
2) Eggs or segments attaches itself
are ingested by pigs to the intestine
or humans. via hooks on
the scolex.
Eggs or tapeworm segments
in feces are passed into
the environment.
Adults in small intestine
This diagram shows the life cycle of a pork tapeworm (Taenia
solium), a human worm parasite. (credit: modification of work
by CDC)
Amensalism
Another type of interaction classified by biologists and ecologists is
amensalism. Amensalism is any interaction between individuals of different
species in which one individual is harmed (-) while the other individual is
not affected (0). For example, as you walk down a side walk on a rainy day
you step on an earthworm; the earthworm is negatively affected, and you
are not affected. Amensalism occurs among micro-organisms when microbe
species A releases chemicals that have a negative effect on microbe species
B, but B has neither a positive nor negative effect on A.
Coevolution
When the genetic change in one species causes a subsequent change in the
genetic structure of another species, this is called coevolution. In a
community, all the interacting species have the potential to influence one
another, and in a sense they are all evolving together. However, coevolution
can only describe genetic changes in interacting species if scientists can
demonstrate that specific interactions result in reciprocal adaptations. For
example, a species of plant may rely solely on one species of insect for
pollination and that one species of insect may only consume nectar from
that one flower. Many of the above examples of species interactions do not
fit the strict definition of coevolution, but one can not argue that these
species are evolving in response to one another and their environment.
Characteristics of Communities
Communities are complex entities that can be characterized by their
structure (the types and numbers of species present) and dynamics (how
communities change over time). Understanding community structure and
dynamics enables community ecologists to manage ecosystems more
effectively.
Foundation Species
Foundation species are considered the “base” or “bedrock” of a community,
having the greatest influence on its overall structure. They are usually the
primary producers: organisms that bring most of the energy into the
community. Kelp, brown algae, is a foundation species, forming the basis of
the kelp forests off the coast of California.
Foundation species may physically modify the environment to produce and
maintain habitats that benefit the other organisms that use them. An
example is the photosynthetic corals of the coral reef ({link]). Corals
themselves are not photosynthetic, but harbor symbionts within their body
tissues (dinoflagellates called zooxanthellae) that perform photosynthesis;
this is another example of a mutualism. The exoskeletons of living and dead
coral make up most of the reef structure, which protects many other species
from waves and ocean currents.
Coral is the foundation
species of coral reef
ecosystems. (credit: Jim E.
Maragos, USFWS)
Biodiversity, Species Richness, and Relative Species Abundance
Biodiversity describes a community’s biological complexity: it is measured
by the number of different species (species richness) in a particular area and
their relative abundance (species evenness). The area in question could be a
habitat, a biome, or the entire biosphere. Species richness is the term that is
used to describe the number of species living in a habitat or biome. Species
richness varies across the globe ({link]). One factor in determining species
richness is latitude, with the greatest species richness occurring in
ecosystems near the equator, which often have warmer temperatures, large
amounts of rainfall, and low seasonality. The lowest species richness occurs
near the poles, which are much colder, drier, and thus less conducive to life
in Geologic time (time since glaciations). The predictability of climate or
productivity is also an important factor. Other factors influence species
richness as well. Relative species abundance is the number of individuals in
a species relative to the total number of individuals in all species within a
habitat, ecosystem, or biome. Foundation species often have the highest
relative abundance of species.
Number of mammal
species per sq km
Coo I 94-128
({) 1-23 MM 129-154
[Ej 24-42 GM 155-178
3 43-60 Mi 179-228
Gi 61-93
The greatest species richness for
mammals in North and South
America is associated with the
equatorial latitudes. (credit:
modification of work by NASA,
CIESIN, Columbia University)
Keystone Species
A keystone species is one species that has a disproportionately large effect
on community structure relative to its biomass or abundance. The intertidal
sea Star, Pisaster ochraceus, of the northwestern United States is a keystone
species ({link]). Studies have shown that when this organism is removed
from communities, populations of their natural prey (mussels) increase,
completely altering the species composition and reducing biodiversity.
Another keystone species is the banded tetra, a fish in tropical streams,
which supplies nearly all of the phosphorus, a necessary inorganic nutrient,
to the rest of the community. If these fish were to become extinct, the
community would be greatly affected.
The Pisaster ochraceus sea
star is a keystone species.
(credit: Jerry Kirkhart)
Note:
Everyday Connection
Invasive Species
Invasive species are non-native organisms that, when introduced to an area
out of their native range, threaten the ecosystem balance of that habitat.
Many such species exist in the United States, as shown in [link]. Whether
enjoying a forest hike, taking a summer boat trip, or simply walking down
an urban street, you have likely encountered an invasive species.
4
+ a a
a re eo
In the United States, invasive species like (a) purple
loosestrife (Lythrum salicaria) and the (b) zebra mussel
(Dreissena polymorpha) threaten certain aquatic
ecosystems. Some forests are threatened by the spread of
(c) common buckthorn (Rhamnus cathartica), (d) garlic
mustard (Alliaria petiolata), and (e) the emerald ash borer
(Agrilus planipennis). The (f) European starling (Sturnus
vulgaris) may compete with native bird species for nest
holes. (credit a: modification of work by Liz West; credit b:
modification of work by M. McCormick, NOAA; credit c:
modification of work by E. Dronkert; credit d: modification
of work by Dan Davison; credit e: modification of work by
USDA; credit f: modification of work by Don DeBold)
One of the many recent proliferations of an invasive species concerns the
growth of Asian carp populations. Asian carp were introduced to the
United States in the 1970s by fisheries and sewage treatment facilities that
used the fish’s excellent filter feeding capabilities to clean their ponds of
excess plankton. Some of the fish escaped, however, and by the 1980s they
had colonized many waterways of the Mississippi River basin, including
the Illinois and Missouri Rivers.
Voracious eaters and rapid reproducers, Asian carp may outcompete native
species for food, potentially leading to their extinction. For example, black
carp are voracious eaters of native mussels and snails, limiting this food
source for native fish species. Silver carp eat plankton that native mussels
and snails feed on, reducing this food source by a different alteration of the
food web. In some areas of the Mississippi River, Asian carp species have
become the most predominant, effectively outcompeting native fishes for
habitat. In some parts of the Illinois River, Asian carp constitute 95 percent
of the community's biomass. Although edible, the fish is bony and not a
desired food in the United States. Moreover, their presence threatens the
native fish and fisheries of the Great Lakes, which are important to local
economies and recreational anglers. Asian carp have even injured humans.
The fish, frightened by the sound of approaching motorboats, thrust
themselves into the air, often landing in the boat or directly hitting the
boaters.
The Great Lakes and their prized salmon and lake trout fisheries are also
being threatened by these invasive fish. Asian carp have already colonized
rivers and canals that lead into Lake Michigan. One infested waterway of
particular importance is the Chicago Sanitary and Ship Channel, the major
supply waterway linking the Great Lakes to the Mississippi River. To
prevent the Asian carp from leaving the canal, a series of electric barriers
have been successfully used to discourage their migration; however, the
threat is significant enough that several states and Canada have sued to
have the Chicago channel permanently cut off from Lake Michigan. Local
and national politicians have weighed in on how to solve the problem, but
no one knows whether the Asian carp will ultimately be considered a
nuisance, like other invasive species such as the water hyacinth and zebra
mussel, or whether it will be the destroyer of the largest freshwater fishery
of the world.
The issues associated with Asian carp show how population and
community ecology, fisheries management, and politics intersect on issues
of vital importance to the human food supply and economy. Socio-political
issues like this make extensive use of the sciences of population ecology
(the study of members of a particular species occupying a particular area
known as a habitat) and community ecology (the study of the interaction of
all species within a habitat).
Community Dynamics
Community dynamics are the changes in community structure and
composition over time. Sometimes these changes are induced by
environmental disturbances such as volcanoes, earthquakes, storms, fires,
and climate change. Communities with a stable structure are said to be at
equilibrium. Following a disturbance, the community may or may not
return to the equilibrium state.
Succession describes the sequential appearance and disappearance of
species in a community over time. In primary succession, newly exposed
or newly formed land is colonized by living things; in secondary
succession, part of an ecosystem is disturbed and remnants of the previous
community remain.
Primary Succession and Pioneer Species
Primary succession occurs when new land is formed or rock is exposed: for
example, following the eruption of volcanoes, such as those on the Big
Island of Hawaii. As lava flows into the ocean, new land is continually
being formed. On the Big Island, approximately 32 acres of land is added
each year. First, weathering and other natural forces break down the
substrate enough for the establishment of certain hearty plants and lichens
with few soil requirements, known as pioneer species ((link]). These
species help to further break down the mineral rich lava into soil where
other, less hardy species will grow and eventually replace the pioneer
species. In addition, as these early species grow and die, they add to an
ever-growing layer of decomposing organic material and contribute to soil
formation. Over time the area will reach an equilibrium state, with a set of
organisms quite different from the pioneer species.
During primary succession in
lava on Maui, Hawaii,
succulent plants are the
pioneer species. (credit:
Forest and Kim Starr)
Secondary succession
A classic example of secondary succession occurs in oak and hickory
forests cleared by wildfire ([link]). Wildfires will burn most vegetation and
kill those animals unable to flee the area. Their nutrients, however, are
returned to the ground in the form of ash. Thus, even when areas are devoid
of life due to severe fires, the area will soon be ready for new life to take
hold.
Before the fire, the vegetation was dominated by tall trees with access to the
major plant energy resource: sunlight. Their height gave them access to
sunlight while also shading the ground and other low-lying species. After
the fire, though, these trees are no longer dominant. Thus, the first plants to
grow back are usually annual plants followed within a few years by quickly
growing and spreading grasses and other pioneer species. Due to, at least in
part, changes in the environment brought on by the growth of the grasses
and other species, over many years, shrubs will emerge along with small
pine, oak, and hickory trees. These organisms are called intermediate
species. Eventually, over 150 years, the forest will reach its equilibrium
point where species composition is no longer changing and resembles the
community before the fire. This equilibrium state is referred to as the
climax community, which will remain stable until the next disturbance.
Secondary Succession of an Oak and Hickory Forest
Am 1 1
a ~ : _ 2 Pelee he
rien. ltl RIN
Pioneer species Intermediate species Climax community
Annual plants grow and are succeeded Shrubs, then pines, and young oak The mature oak and hickory forest
by grasses and perennials. and hickory begin to grow. remains stable until the next disturbance.
Secondary succession is shown in an oak and hickory forest
after a forest fire.
Ecosystem Experimentation and Modeling
"Even if a scientific model, like a car, has only a few years to run before it
is discarded, it serves its purpose for getting from one place to another."
David L. Wingate, "Complex Clocks", Digestive Diseases and Sciences,
1983, 28:1139
Ecosystems are complex entities, with many components and variables, and
thus they present quite a daunting task for ecosystem modelers. Life in an
ecosystem is often about competition for limited resources, a characteristic
of the mechanism of natural selection. Competition in communities (all
living things within specific habitats) is observed both within species and
among different species. The resources for which organisms compete
include organic material from living or previously living organisms,
sunlight, and mineral nutrients, which provide the energy for living
processes and the matter to make up organisms’ physical structures. Other
critical factors influencing community dynamics are the components of its
physical and geographic environment: a habitat’s latitude, amount of
rainfall, topography (elevation), and available species. These are all
important environmental variables that determine which organisms can
exist within a particular area.
Furthermore, ecosystems are routinely exposed to various disturbances, or
changes in the environment that effect their compositions: yearly variations
in rainfall and temperature and the slower processes of plant growth, which
may take several years. Many of these disturbances are a result of natural
processes. For example, when lightning causes a forest fire and destroys
part of a forest ecosystem, the ground is eventually populated by grasses,
then by bushes and shrubs, and later by mature trees, restoring the forest to
its former state. The impact of environmental disturbances caused by
human activities is as important as the changes wrought by natural
processes. Human agricultural practices, air pollution, acid rain, global
deforestation, overfishing, eutrophication, oil spills, and illegal dumping on
land and into the ocean are all issues of concern to conservationists.
Research into Ecosystem Dynamics: Ecosystem
Experimentation and Modeling
The study of the changes in ecosystem structure caused by changes in the
environment (disturbances) or by internal forces is called ecosystem
dynamics. Ecosystems are characterized using a variety of research
methodologies. Some ecologists study ecosystems using controlled
experimental systems, while some study entire ecosystems in their natural
state, and others use both approaches.
A holistic ecosystem model attempts to quantify the composition,
interaction, and dynamics of entire ecosystems; it is the most representative
of the ecosystem in its natural state. A food web is an example of a holistic
ecosystem model. However, this type of study is limited by time and
expense, as well as the fact that it is neither feasible nor ethical to do
experiments on large natural ecosystems. To quantify all different species in
an ecosystem and the dynamics in their habitat is difficult, especially when
studying large habitats such as the Amazon Rainforest, which covers 1.4
billion acres (5.5 million km?) of the Earth’s surface.
For these reasons, scientists study ecosystems under more controlled
conditions. Experimental systems usually involve either partitioning a part
of a natural ecosystem that can be used for experiments, termed a
mesocosm, or by re-creating an ecosystem entirely in an indoor or outdoor
laboratory environment, which is referred to as a microcosm. A major
limitation to these approaches is that removing individual organisms from
their natural ecosystem or altering a natural ecosystem through partitioning
may change the dynamics of the ecosystem. These changes are often due to
differences in species numbers and diversity and also to environment
alterations caused by partitioning (mesocosm) or re-creating (microcosm)
the natural habitat. Thus, these types of experiments are not totally
predictive of changes that would occur in the ecosystem from which they
were gathered.
As both of these approaches have their limitations, some ecologists suggest
that results from these experimental systems should be used only in
conjunction with holistic ecosystem studies to obtain the most
representative data about ecosystem structure, function, and dynamics.
Scientists use the data generated by these experimental studies to develop
ecosystem models that demonstrate the structure and dynamics of
ecosystems. Three basic types of ecosystem modeling are routinely used in
research and ecosystem management: a conceptual model, an analytical
model, and a simulation model. A conceptual model is an ecosystem model
that consists of flow charts to show interactions of different compartments
of the living and nonliving components of the ecosystem. A conceptual
model describes ecosystem structure and dynamics and shows how
environmental disturbances affect the ecosystem; however, its ability to
predict the effects of these disturbances is limited. Analytical and
simulation models, in contrast, are mathematical methods of describing
ecosystems that are indeed capable of predicting the effects of potential
environmental changes without direct experimentation, although with some
limitations as to accuracy. An analytical model is an ecosystem model that
is created using simple mathematical formulas to predict the effects of
environmental disturbances on ecosystem structure and dynamics. A
simulation model is an ecosystem model that is created using complex
computer algorithms to holistically model ecosystems and to predict the
effects of environmental disturbances on ecosystem structure and dynamics.
Ideally, these models are accurate enough to determine which components
of the ecosystem are particularly sensitive to disturbances, and they can
Serve as a guide to ecosystem managers (such as conservation ecologists or
fisheries biologists) in the practical maintenance of ecosystem health.
Conceptual Models
Conceptual models are useful for describing ecosystem structure and
dynamics and for demonstrating the relationships between different
organisms in a community and their environment. Conceptual models are
usually depicted graphically as flow charts. The organisms and their
resources are grouped into specific compartments with arrows showing the
relationship and transfer of energy or nutrients between them.
To model the cycling of mineral nutrients, organic and inorganic nutrients
are subdivided into those that are bioavailable (ready to be incorporated into
biological macromolecules) and those that are not. For example, in a
terrestrial ecosystem near a deposit of coal, carbon will be available to the
plants of this ecosystem as carbon dioxide gas in a short-term period, not
from the carbon-rich coal itself. However, over a longer period,
microorganisms capable of digesting coal will incorporate its carbon or
release it as natural gas (methane, CH,), changing this unavailable organic
source into an available one. This conversion is greatly accelerated by the
combustion of fossil fuels by humans, which releases large amounts of
carbon dioxide into the atmosphere. This is thought to be a major factor in
the rise of the atmospheric carbon dioxide levels in the industrial age. The
carbon dioxide released from burning fossil fuels is produced faster than
photosynthetic organisms can use it. This process is intensified by the
reduction of photosynthetic trees because of worldwide deforestation. Most
scientists agree that high atmospheric carbon dioxide is a major cause of
global climate change.
Analytical and Simulation Models
The major limitation of conceptual models is their inability to predict the
consequences of changes in ecosystem species and/or environment.
Ecosystems are dynamic entities and subject to a variety of abiotic and
biotic disturbances caused by natural forces and/or human activity.
Ecosystems altered from their initial equilibrium state can often recover
from such disturbances and return to a state of equilibrium. As most
ecosystems are subject to periodic disturbances and are often in a state of
change, they are usually either moving toward or away from their
equilibrium state. There are many of these equilibrium states among the
various components of an ecosystem, which affects the ecosystem overall.
Furthermore, as humans have the ability to greatly and rapidly alter the
species content and habitat of an ecosystem, the need for predictive models
that enable understanding of how ecosystems respond to these changes
becomes more crucial.
Analytical models often use simple, linear components of ecosystems, such
as food chains, and are known to be complex mathematically; therefore,
they require a significant amount of mathematical knowledge and expertise.
Although analytical models have great potential, their simplification of
complex ecosystems is thought to limit their accuracy. Simulation models
that use computer programs are better able to deal with the complexities of
ecosystem structure.
A recent development in simulation modeling uses supercomputers to
create and run individual-based simulations, which accounts for the
behavior of individual organisms and their effects on the ecosystem as a
whole. These simulations are considered to be the most accurate and
predictive of the complex responses of ecosystems to disturbances.
Nitrogen and Phosphorus Cycles
"As mouths multiply, food resources dwindle. Land is a limited quantity,
and the land that will grow wheat is absolutely dependent on difficult and
capricious natural phenomena... I have to point the way out of this colossal
dilemma. It is the chemist who must come to the rescue of the threatened
communities. It is through the laboratory that starvation may ultimately be
turned into plenty... The fixation of atmospheric nitrogen is one of the great
discoveries, awaiting the genius of chemists." William Crookes, Chemical
News. 1898, 78:125.
The "difficult and capricious natural phenomena" of nitrogen fixation is just
one part of the biogeochemical cycle of this nutrient, but it is, as Crookes
noted, an extremely important part. Chemists have succeeded in the quest to
develop reactions that can fix atmospheric nitrogen into forms that can be
used by living organisms, but it should be noted that humble
microorganisms did this long before boastful chemists thought about it.
Industrial processes for nitrogen fixation now produce as much usable
nitrogen as all of the biological nitrogen-fixers on the planet. This chemical
success, however, does come with some undesirable consequences, as you
will learn below.
Energy flows directionally through ecosystems, entering as sunlight (or
inorganic molecules for chemoautotrophs) and leaving as heat during the
many transfers between trophic levels. However, the matter that makes up
living organisms is conserved and recycled. The six most common elements
associated with organic molecules—carbon, nitrogen, hydrogen, oxygen,
phosphorus, and sulfur—take a variety of chemical forms and may exist for
long periods in the atmosphere, on land, in water, or beneath the Earth’s
surface. Geologic processes, such as weathering, erosion, water drainage,
and the subduction of the continental plates, all play a role in this recycling
of materials. Because geology and chemistry have major roles in the study
of this process, the recycling of inorganic matter between living organisms
and their environment is called a biogeochemical cycle.
The Nitrogen Cycle
Nitrogen is an essential nutrient for living processes; it is a major
component of proteins and nucleic acids. Proteins are important biological
molecules because all cellular activities are driven by proteins. Nucleic
acids are the building blocks of DNA (hereditary material). Nitrogen is
often the limiting nutrient (necessary for growth) on terrestrial ecosystems
[link].
Getting nitrogen into the living world is difficult. Plants and phytoplankton
are not equipped to incorporate nitrogen from the atmosphere (which exists
as tightly bonded, triple covalent N>) even though this molecule comprises
approximately 78 percent of the atmosphere. Nitrogen enters the living
world via free-living and symbiotic bacteria, which incorporate nitrogen
into their macromolecules through nitrogen fixation (conversion of N>).
Cyanobacteria live in most aquatic ecosystems where sunlight is present;
they play a key role in nitrogen fixation. Cyanobacteria are able to use
inorganic sources of nitrogen to “fix” nitrogen. Rhizobium bacteria live
symbiotically in the root nodules of legumes (such as peas, beans, and
peanuts) and provide them with the organic nitrogen they need. Free-living
bacteria, such as Azotobacter, are also important nitrogen fixers. In addition
to natural nitrogen fixation by microbes, humans industrially fix nitrogen to
produce artificial fertilizers.
Organic nitrogen is especially important to the study of ecosystem
dynamics since many ecosystem processes, such as primary production and
decomposition, are limited by the available supply of nitrogen. As shown in
[link], the nitrogen that enters living systems by nitrogen fixation is
successively converted from organic nitrogen back into nitrogen gas by
bacteria. This process occurs in three steps in terrestrial systems:
ammonification, nitrification, and denitrification. First, the ammonification
process converts nitrogenous waste from living animals or from the remains
of dead animals into ammonium (NH,") by certain bacteria and fungi.
Second, the ammonium is converted to nitrites (NO> _) by nitrifying
bacteria, such as Nitrosomonas, through nitrification. Subsequently, nitrites
are converted to nitrates (NO3_) by similar organisms. Third, the process of
denitrification occurs, whereby bacteria, such as Pseudomonas and
Clostridium, convert the nitrates into nitrogen gas, allowing it to re-enter
the atmosphere.
The Whit EhyCyvele
Denitrification
by bacteria
/\
fm
|
J
Nitrification by Nitrogenous
bacteria to NO; wastes in soil
V
- ee Ammonification Nitrogen
Nitrification by «4 _____ by bacteria and << fixation
bacteria to NOZ > fungi to NH,* S ~ by bacteria
Nitrogen enters the living world from the atmosphere via
nitrogen-fixing bacteria. This nitrogen and nitrogenous waste
from animals is then processed back into gaseous nitrogen by
soil bacteria, which also supply terrestrial food webs with the
organic nitrogen they need. (credit: modification of work by
John M. Evans and Howard Perlman, USGS)
Human activity can release nitrogen into the environment by two primary
means: the combustion of fossil fuels, which releases different nitrogen
oxides, and by the use of artificial fertilizers in agriculture, which are then
washed into lakes, streams, and rivers by surface runoff. Atmospheric
nitrogen is associated with several effects on Earth’s ecosystems including
the production of acid rain (as nitric acid, HNO3) and greenhouse gas (as
nitrous oxide, N»O) potentially causing climate change. A major effect from
fertilizer runoff is saltwater and freshwater eutrophication, a process
whereby nutrient runoff causes the excess growth of microorganisms,
depleting dissolved oxygen levels and killing ecosystem fauna.
A similar process occurs in the marine nitrogen cycle, where the
ammonification, nitrification, and denitrification processes are performed
by marine bacteria. Some of this nitrogen falls to the ocean floor as
sediment, which can then be moved to land in geologic time by uplift of the
Earth’s surface and thereby incorporated into terrestrial rock. Although the
movement of nitrogen from rock directly into living systems has been
traditionally seen as insignificant compared with nitrogen fixed from the
atmosphere, a recent study showed that this process may indeed be
significant and should be included in any study of the global nitrogen cycle.
[footnote]
Scott L. Morford, Benjamin Z. Houlton, and Randy A. Dahlgren,
“Increased Forest Ecosystem Carbon and Nitrogen Storage from Nitrogen
Rich Bedrock,” Nature 477, no. 7362 (2011): 78-81.
The Phosphorus Cycle
Phosphorus is another essential nutrient for living processes; it is a major
component of nucleic acids, phospholipids, and, as calcium phosphate,
makes up the supportive components of our bones. Phosphorus is often the
limiting nutrient (necessary for growth) in aquatic ecosystems ([link]).
Phosphorus occurs in nature as the phosphate ion (PO,° ). In addition to
phosphate runoff as a result of human activity (mined to make artificial
fertilizers), natural surface runoff occurs when it is leached from phosphate-
containing rock by weathering, thus sending phosphates into rivers, lakes,
and the ocean. This rock has its origins in the ocean. Phosphate-containing
ocean sediments form primarily from the bodies of ocean organisms and
from their excretions. However, in remote regions, volcanic ash, aerosols,
and mineral dust may also be significant phosphate sources. This sediment
then is moved to land over geologic time by the uplifting of areas of the
Earth’s surface.
Phosphorus is also reciprocally exchanged between phosphate dissolved in
the ocean and marine ecosystems. The movement of phosphate from the
ocean to the land and through the soil is extremely slow, with the average
phosphate ion having an oceanic residence time between 20,000 and
100,000 years.
In nature, phosphorus exists as the phosphate ion (PO,° ).
Weathering of rocks and volcanic activity releases phosphate
into the soil, water, and air, where it becomes available to
terrestrial food webs. Phosphate enters the oceans via surface
runoff, groundwater flow, and river flow. Phosphate dissolved
in ocean water cycles into marine food webs. Some phosphate
from the marine food webs falls to the ocean floor, where it
forms sediment. (credit: modification of work by John M.
Evans and Howard Perlman, USGS)
Excess phosphorus and nitrogen that enters these ecosystems from fertilizer
runoff and from sewage causes excessive growth of microorganisms and
depletes the dissolved oxygen, which leads to the death of many ecosystem
fauna, such as shellfish and finfish. This process is responsible for dead
zones in lakes and at the mouths of many major rivers ([link]).
Particulate Organic Carbon (mg/m') Population Density (persons/km’) Dead Zone Size (km’)
unkown « . +
10 20 $0 100 ©6200 $00 1,000 ! 10 100 1,000 10k 100k 0.1 + 10 100 Ik 10k
Dead zones occur when phosphorus and nitrogen from
fertilizers cause excessive growth of microorganisms, which
depletes oxygen and kills fauna. Worldwide, large dead zones
are found in coastal areas of high population density. (credit:
NASA Earth Observatory)
A dead zone is an area within a freshwater or marine ecosystem where
large areas are depleted of their normal flora and fauna; these zones can be
caused by eutrophication, oil spills, dumping of toxic chemicals, and other
human activities. The number of dead zones has been increasing for several
years, and more than 400 of these zones were present as of 2008. One of the
worst dead zones is off the coast of the United States in the Gulf of Mexico,
where fertilizer runoff from the Mississippi River basin has created a dead
zone of over 8463 square miles. Phosphate and nitrate runoff from
fertilizers also negatively affect several lake and bay ecosystems including
the Chesapeake Bay in the eastern United States.
Note:
Everyday Connection
Chesapeake Bay
(a)
This (a) satellite image shows
the Chesapeake Bay, an
ecosystem affected by
phosphate and nitrate runoff. A
(b) member of the Army Corps
of Engineers holds a clump of
oysters being used as a part of
the oyster restoration effort in
the bay. (credit a: modification
of work by NASA/MODIS;
credit b: modification of work
by U.S. Army)
The Chesapeake Bay has long been valued as one of the most scenic areas
on Earth; it is now in distress and is recognized as a declining ecosystem.
In the 1970s, the Chesapeake Bay was one of the first ecosystems to have
identified dead zones, which continue to kill many fish and bottom-
dwelling species, such as clams, oysters, and worms. Several species have
declined in the Chesapeake Bay due to surface water runoff containing
excess nutrients from artificial fertilizer used on land. The source of the
fertilizers (with high nitrogen and phosphate content) is not limited to
agricultural practices. There are many nearby urban areas and more than
150 rivers and streams empty into the bay that are carrying fertilizer runoff
from lawns and gardens. Thus, the decline of the Chesapeake Bay is a
complex issue and requires the cooperation of industry, agriculture, and
everyday homeowners.
Of particular interest to conservationists is the oyster population; it is
estimated that more than 200,000 acres of oyster reefs existed in the bay in
the 1700s, but that number has now declined to only 36,000 acres. Oyster
harvesting was once a major industry for Chesapeake Bay, but it declined
88 percent between 1982 and 2007. This decline was due not only to
fertilizer runoff and dead zones but also to overharvesting. Oysters require
a certain minimum population density because they must be in close
proximity to reproduce. Human activity has altered the oyster population
and locations, greatly disrupting the ecosystem.
The restoration of the oyster population in the Chesapeake Bay has been
ongoing for several years with mixed success. Not only do many people
find oysters good to eat, but they also clean up the bay. Oysters are filter
feeders, and as they eat, they clean the water around them. In the 1700s, it
was estimated that it took only a few days for the oyster population to filter
the entire volume of the bay. Today, with changed water conditions, it is
estimated that the present population would take nearly a year to do the
same job.
Restoration efforts have been ongoing for several years by non-profit
organizations, such as the Chesapeake Bay Foundation. The restoration
goal is to find a way to increase population density so the oysters can
reproduce more efficiently. Many disease-resistant varieties (developed at
the Virginia Institute of Marine Science for the College of William and
Mary) are now available and have been used in the construction of
experimental oyster reefs. Efforts to clean and restore the bay by Virginia
and Delaware have been hampered because much of the pollution entering
the bay comes from other states, which stresses the need for inter-state
cooperation to gain successful restoration.
The new, hearty oyster strains have also spawned a new and economically
viable industry—oyster aquaculture—which not only supplies oysters for
food and profit, but also has the added benefit of cleaning the bay.
Freshwater Biomes
Introduction
"For as the element of water lies in the middle of the globe, so, the branches
run out from the root in its circuit on all sides towards the plains and
towards the light. From this root very many branches are born." Paracelsus,
"The Philosophy of the Generation of the Elements", Book the Fourth, Text
II. In The Hermetic and Alchemical Writings of Aureolus Phillipus
Theophrastus Bombast, of Hohenheim, called Paracelsus the Great,
translated by A.E. Waite (1894), 1:232.
The alchemical thinking of Paracelsus might seem unscientific today, but
his insights about the central nature of water are still viable. Freshwater
biomes are among the most important on the planet in terms of species
diversity and ecosystem services. Abiotic and biotic (including human)
impacts on these biomes are among the most important factors in
influencing these functions, and their role in the various biogeochemical
cycles cannot be overstated.
Abiotic Factors Influencing Aquatic Biomes
Aquatic biomes are influenced by a series of abiotic factors associated with
water, and these factors include the amount of light, stratification due to
temperature, and the thermal properties of water. Another abiotic factor is
nutrients, review the following information about freshwater biomes and
begin to think about how human disturbances can affect freshwater
ecosystems.
Freshwater Biomes
Freshwater biomes include lakes and ponds (standing water) as well as
rivers and streams (flowing water). They also include wetlands, which will
be discussed later. Humans rely on freshwater biomes to provide aquatic
resources for drinking water, crop irrigation, sanitation, and industry. These
various roles and human benefits are referred to as ecosystem services.
Lakes and ponds are found in terrestrial landscapes and are, therefore,
connected with abiotic and biotic factors influencing these terrestrial
biomes.
Lakes and Ponds
Lakes and ponds can range in area from a few square meters to thousands
of square kilometers. Temperature is an important abiotic factor affecting
living things found in lakes and ponds. In the summer, thermal stratification
of lakes and ponds occurs when the upper layer of water is warmed by the
sun and does not mix with deeper, cooler water. Light can penetrate within
the photic zone of the lake or pond. Phytoplankton (algae and
cyanobacteria) are found here and carry out photosynthesis, providing the
base of the food web of lakes and ponds. Zooplankton, such as rotifers and
small crustaceans, consume these phytoplankton. At the bottom of lakes
and ponds, bacteria in the aphotic zone break down dead organisms that
sink to the bottom.
Nitrogen and phosphorus are important limiting nutrients in lakes and
ponds. Because of this, they are determining factors in the amount of
phytoplankton growth in lakes and ponds. When there is a large input of
nitrogen and phosphorus (from sewage and runoff from fertilized lawns and
farms, for example), the growth of algae skyrockets, resulting in a large
accumulation of algae called an algal bloom. Algal blooms can become so
extensive that they reduce light penetration in water. As a result, the lake or
pond becomes aphotic and photosynthetic plants cannot survive. When the
algae die and decompose, severe oxygen depletion of the water occurs.
Fishes and other organisms that require oxygen are then more likely to die,
and resulting dead zones are found across the globe. Lake Erie and the Gulf
of Mexico represent freshwater and marine habitats where phosphorus
control and storm water runoff pose significant environmental challenges.
Rivers and Streams
Rivers and streams are continuously moving bodies of water that carry large
amounts of water from the source, or headwater, to a lake or ocean. The
largest rivers include the Nile River in Africa, the Amazon River in South
America, and the Mississippi River in North America.
Abiotic features of rivers and streams vary along the length of the river or
stream. Streams begin at a point of origin referred to as source water. The
source water is usually cold, low in nutrients, and clear. The channel (the
width of the river or stream) is narrower than at any other place along the
length of the river or stream. Because of this, the current is often faster here
than at any other point of the river or stream.
The fast-moving water results in minimal silt accumulation at the bottom of
the river or stream; therefore, the water is clear. Photosynthesis here is
mostly attributed to algae that are growing on rocks; the swift current
inhibits the growth of phytoplankton. An additional input of energy can
come from leaves or other organic material that falls into the river or stream
from trees and other plants that border the water. When the leaves
decompose, the organic material and nutrients in the leaves are returned to
the water. Plants and animals have adapted to this fast-moving water. For
instance, leeches (phylum Annelida) have elongated bodies and suckers on
both ends. These suckers attach to the substrate, keeping the leech anchored
in place. Freshwater trout species (phylum Chordata) are an important
predator in these fast-moving rivers and streams.
As the river or stream flows away from the source, the width of the channel
gradually widens and the current slows. This slow-moving water, caused by
the gradient decrease and the volume increase as tributaries unite, has more
sedimentation. Phytoplankton can also be suspended in slow-moving water.
Therefore, the water will not be as clear as it is near the source. The water is
also warmer. Worms (phylum Annelida) and insects (phylum Arthropoda)
can be found burrowing into the mud. The higher order predator vertebrates
(phylum Chordata) include waterfowl, frogs, and fishes. These predators
must find food in these slow moving, sometimes murky, waters and, unlike
the trout in the waters at the source, these vertebrates may not be able to use
vision as their primary sense to find food. Instead, they are more likely to
use taste or chemical cues to find prey.
Wetlands
Wetlands are environments in which the soil is either permanently or
periodically saturated with water. Wetlands are different from lakes because
wetlands are shallow bodies of water whereas lakes vary in depth. Emergent
vegetation consists of wetland plants that are rooted in the soil but have
portions of leaves, stems, and flowers extending above the water’s surface.
There are several types of wetlands including marshes, swamps, bogs,
mudflats, and salt marshes. The three shared characteristics among these
types—what makes them wetlands—are their hydrology, hydrophytic
vegetation, and hydric soils.
Freshwater marshes and swamps are characterized by slow and steady
water flow. Bogs develop in depressions where water flow is low or
nonexistent. Bogs usually occur in areas where there is a clay bottom with
poor percolation. Percolation is the movement of water through the pores in
the soil or rocks. The water found in a bog is stagnant and oxygen depleted
because the oxygen that is used during the decomposition of organic matter
is not replaced. As the oxygen in the water is depleted, decomposition
slows. This leads to organic acids and other acids building up and lowering
the pH of the water. At a lower pH, nitrogen becomes unavailable to plants.
This creates a challenge for plants because nitrogen is an important limiting
resource. Some types of bog plants (such as sundews, pitcher plants, and
Venus flytraps) capture insects and extract the nitrogen from their bodies.
Bogs have low net primary productivity because the water found in bogs
has low levels of nitrogen and oxygen.
Population Growth Curves
Introduction
"Population, when unchecked, increases in a geometrical ratio. Subsistence
increases only in an arithmetical ratio. A slight acquaintance with numbers
will show the immensity of the first power in comparison with the second."
Thomas Malthus, An Essay on the Principle of Populations, 1798
Malthus recognized the fact that there is a connection between resources
and population growth, and that one of these (population growth) can
increase at a greater rate than the other. Modern population ecologists make
use of a variety of methods to model population dynamics mathematically.
These more precise models can then be used to accurately describe changes
occurring in a population and better predict future changes. Use the
following information to make sure that you have at least a "slight
acquaintance" with the mathematical principles that are used to describe
population growth.
Exponential Growth
Charles Darwin, in his theory of natural selection, was greatly influenced by
the English clergyman Thomas Malthus. Malthus published a book in 1798
stating that populations with unlimited natural resources grow very rapidly.
This accelerating pattern of increasing population size is called exponential
growth.
The best example of exponential growth is seen in bacteria. Some species of
Bacteria can undergo cell division about every hour. If 1000 bacteria are
placed in a large flask with an unlimited supply of nutrients (so the nutrients
will not become depleted), after an hour, there is one round of division and
each organism divides, resulting in 2000 organisms—an increase of 1000.
In another hour, each of the 2000 organisms will double, producing 4000,
an increase of 2000 organisms. After the third hour, there should be 8000
bacteria in the flask, an increase of 4000 organisms. The important concept
of exponential growth is that the population growth rate—the number of
organisms added in each reproductive generation—is accelerating; that is, it
is increasing at a greater and greater rate. After 1 day and 24 of these
cycles, the population would have increased from 1000 to more than 16
billion. When the population size, N, is plotted over time, a J-shaped
growth curve is produced ([link]).
Exponential growth is common when population organisms have unlimited
resources. The growth of that population can be calculated using the
equation below. For further explanation of this equation please go to
Population Growth .
Equation:
G=rN
The value "r” can be positive, meaning the population is increasing in size;
or negative, meaning the population is decreasing in size; or zero, where the
population’s size is unchanging, a condition known as zero population
growth. A further refinement of the formula recognizes that different
species have inherent differences in their per capita growth rates (r), even
under ideal conditions. Obviously, a bacterium can reproduce more rapidly
and have a higher per capita growth rate than a human. The maximal
growth rate for a species is its biotic potential, or r,,,,, thus changing the
equation to:
Equation:
G = TmaxN
© co)
N N
n wn
i= c
2 iS]
& &
S =
a a
{o) [o)
a a
When resources are unlimited, populations exhibit
exponential growth, resulting in a J-shaped curve.
When resources are limited, populations exhibit
logistic growth. In logistic growth, population
expansion decreases as resources become scarce, and
it levels off when the carrying capacity of the
environment is reached, resulting in an S-shaped
curve.
Logistic Growth
Exponential growth is possible only when infinite natural resources are
available; this is not the case in the real world. Charles Darwin recognized
this fact in his description of the “struggle for existence,” which states that
individuals will compete (with members of their own or other species) for
limited resources. The successful ones will survive to pass on their own
characteristics and traits (which we know now are transferred by genes) to
the next generation at a greater rate (natural selection). To model the reality
of limited resources, population ecologists developed the logistic growth
model.
Carrying Capacity and the Logistic Model
In the real world, with its limited resources, exponential growth cannot
continue indefinitely. Exponential growth may occur in environments where
there are few individuals and plentiful resources, but when the number of
individuals gets large enough, resources will be depleted, slowing the
growth rate. Eventually, the growth rate will plateau or level off ((link]).
This population size, which represents the maximum population size that a
particular environment can support, is called the carrying capacity, or K.
The formula we use to calculate logistic growth adds the carrying capacity
as a moderating force in the growth rate. The expression “K — N” is
indicative of how many individuals may be added to a population at a given
stage, and “K — N” divided by “K” is the fraction of the carrying capacity
available for further growth. Thus, the exponential growth model is
restricted by this factor to generate the logistic growth equation:
Equation:
(K — N)
G =TmaxlV 7
Notice that when N is very small, (K-N)/K becomes close to K/K or 1, and
the right side of the equation reduces to rj4,V, which means the population
is growing exponentially and is not influenced by carrying capacity. On the
other hand, when N is large, (K-N)/K come close to zero, which means that
population growth will be slowed greatly or even stopped. Thus, population
growth is greatly slowed in large populations by the carrying capacity K.
This model also allows for the population of a negative population growth,
or a population decline. This occurs when the number of individuals in the
population exceeds the carrying capacity (because the value of (K-N)/K is
negative).
A graph of this equation yields an S-shaped curve ({link]), and it is a more
realistic model of population growth than exponential growth. There are
three different sections to an S-shaped curve. Initially, growth is exponential
because there are few individuals and ample resources available. Then, as
resources begin to become limited, the growth rate decreases. Finally,
growth levels off at the carrying capacity of the environment, with little
change in population size over time.
Introduction to Water Pollution
The Water Pollution Crisis
Introduction
Pollution, pollution,
You can use the latest toothpaste,
And then rinse your mouth with industrial waste.
Tom Lehrer, lyrics from his 1965 song Pollution
The effects humans have on the water cycle and fresh water supply
described one aspect of the global water crisis, specifically the water
shortages that afflict many arid and densely populated areas. The global
water crisis also involves water pollution, because to be useful for drinking
and irrigation, water must not be polluted beyond certain thresholds.
According to the World Health Organization, in 2008 approximately 880
million people in the world (or 13% of world population) did not have
access to improved (safe) drinking water (World Health Statistics, 2010)
({link]). At the same time, about 2.6 billion people (or 40% of world
population) lived without improved sanitation ([link]), which is defined as
having access to a public sewage system, septic tank, or even a simple pit
latrine. Each year approximately 1.7 million people die from diarrheal
diseases associated with unsafe drinking water, inadequate sanitation, and
poor hygiene, e.g., hand washing with soap. Almost all of these deaths are
in developing countries, and around 90% of them occur among children
under the age of 5 (see Figure [link]). Compounding the water crisis is the
issue of social justice; poor people more commonly lack clean water and
Sanitation than wealthy people in similar areas. Globally, improving water,
sanitation, and hygiene could prevent up to 9% of all disease and 6% of all
deaths. In addition to the global waterborne disease crisis, chemical
pollution from agriculture, industry, cities, and mining threatens global
water quality. Some chemical pollutants have serious and well-known
health effects; however, many others have poorly known long-term health
effects. In the U.S. currently more than 40,000 water bodies fit the
definition of “impaired” set by EPA (See Figure [link]), which means they
could neither support a healthy ecosystem nor meet water quality standards.
In Gallup public polls conducted over the past decade Americans
consistently put water pollution and water supply as the top environmental
concerns over issues such as air pollution, deforestation, species extinction,
and global warming.
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Proportion of Population by Country Using Improved Drinking
Water Sources in 2008 Improved drinking water sources, e.g.,
household connections, public standpipes, boreholes, protected dug
wells and springs, and rainwater collections, are defined as those more
likely to provide safe water than unimproved water sources, e.g.,
unprotected wells and springs, vendor-provided water, bottled water
(unless water for other uses is available from an improved source), and
tanker truck-provided water. Source: World Health Organization
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Proportion of Population by Country Using Improved Sanitation
Facilities in 2008 Improved sanitation facilities, e.g., connection to
public sewers or septic systems, pour-flush latrines, pit latrines, and
ventilated improved pit latrines, are defined as those more likely to be
sanitary than unimproved facilities, e.g., bucket latrines, public
latrines, and open pit latrines. Source: World Health Organization
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Deaths by Country from Diarrhea Caused by Unsafe Water,
Unimproved Sanitation, and Poor Hygiene in Children Less than 5
Years Old, 2004 Source: World Health Organization
Impaired 9“
Waters-1998 R
(Updated Feb. 2000)
No Waters Listed
me <5%
Ge 5 - 10%
We 10-25%
Ma > 25%
Percentage of Impaired Water Bodies in a Watershed by State
in USA Based on US EPA Data in 2000 Map of watersheds
containing impaired water bodies from the U.S. Environmental
Protection Agency's 1998 list of impaired waters Source: U.S.
Geological Survey
Water Chemistry Overview
Compared to other molecules of similar molecular weight, water (H2O) has
unique physical properties including high values for melting and boiling
point, surface tension (water’s cohesion, or “stickiness”), and capacity to
dissolve soluble minerals, i.e., act as a solvent. These properties are related
to its asymmetrical structure and polar nature, which means it is electrically
neutral overall but it has a net positive charge on the side with the two
hydrogen atoms and a net negative charge on the oxygen side ({link]). This
separation of the electrical charge within a water molecule results in
hydrogen bonds with other water molecules, mineral surfaces (hydrogen
bonding produces the water films on minerals in the unsaturated zone of the
subsurface), and dissolved ions (atoms with a negative or positive charge).
Many minerals and pollutants dissolve readily in water because water forms
hydration shells (spheres of loosely coordinated, oriented water molecules)
around ions.
Hydrogen
bonds
Structure of Water, Polar Charge of Water,
and Hydrogen Bonds between Water
Molecules Source: Michal Maras at
Wikimedia Commons
Any natural water contains dissolved chemicals; some of these are
important human nutrients, while others can be harmful to human health.
The abundance of a water pollutant is commonly given in very small
concentration units such as parts per million (ppm) or even parts per billion
(ppb). An arsenic concentration of 1 ppm means 1 part of arsenic per
million parts of water. This is equivalent to one drop of arsenic in 50 liters
of water. To give you a different perspective on appreciating small
concentration units, converting 1 ppm to length units is 1 cm (0.4 in) in 10
km (6 miles) and converting 1 ppm to time units is 30 seconds in a year.
Total dissolved solids (TDS) represent the total amount of dissolved
material in water. Average TDS (salinity) values for rainwater, river water,
and seawater are about 4 ppm, 120 ppm, and 35,000 ppm. The most
important processes that affect the salinity of natural waters are
evaporation, which distills nearly pure water and leaves the dissolved ions
in the original water, and chemical weathering, which involves mineral
dissolution that adds dissolved ions to water. Fresh water is commonly
defined as containing less than either 1,000 or 500 ppm TDS, but the US
Environmental Protection Agency (EPA) recommends that drinking water
not exceed 500 ppm TDS or else it will have an unpleasant salty taste.
Water Pollution Overview
Water pollution is the contamination of water by an excess amount of a
substance that can cause harm to human beings and the ecosystem. The
level of water pollution depends on the abundance of the pollutant, the
ecological impact of the pollutant, and the use of the water. Pollutants are
derived from biological, chemical, or physical processes. Although natural
processes such as volcanic eruptions or evaporation sometimes can cause
water pollution, most pollution is derived from human, land-based activities
(see Figure [link]). Water pollutants can move through different water
reservoirs, as the water carrying them progresses through stages of the
water cycle (see Figure [link]). Water residence time (the average time that
a water molecule spends in a water reservoir) is very important to pollution
problems because it affects pollution potential. Water in rivers has a
relatively short residence time, so pollution usually is there only briefly. Of
course, pollution in rivers may simply move to another reservoir, such as
the ocean, where it can cause further problems. Groundwater is typically
characterized by slow flow and longer residence time, which can make
groundwater pollution particularly problematic. Finally, pollution residence
time can be much greater than the water residence time because a pollutant
may be taken up for a long time within the ecosystem or absorbed onto
sediment.
Water Pollution Obvious water pollution in
the form of floating debris; invisible water
pollutants sometimes can be much more
harmful than visible ones. Source: Stephen
Codrington at Wikimedia Commons
Point-source contamination can ution spreads across the landscape
be traced to specific points of en overlooked as a major nonpoint
discharge from wastewater of pollution. Airborne nutrients and
treatment plants and factories or can be transported far from their
from combined sewers. area of origin.
atte
soil and sediment
transport considerable
amounts of some nutrients,
ciel such as organic nitrogen and
phosphorus, and some
pesticides, such as DDT,
to rivers and streams.
SEEPAGE GROUND-WATER SEEPAGE
DISCHARGE
TO STREAMS
Sources of Water Contamination Sources of some water pollutants
and movement of pollutants into different water reservoirs of the water
cycle. Source: U.S. Geological Survey
Pollutants enter water supplies from point sources, which are readily
identifiable and relatively small locations, or nonpoint sources, which are
large and more diffuse areas. Point sources of pollution include animal
“factory” farms that raise a large number and high density of livestock such
as cows, pigs, and chickens ([link]) and discharge pipes from a factories or
sewage treatment plants. Combined sewer systems that have a single set of
underground pipes to collect both sewage and storm water runoff from
streets for wastewater treatment can be major point sources of pollutants.
During heavy rain, storm water runoff may exceed sewer capacity, causing
it to back up and spilling untreated sewage into surface waters ((link]).
Nonpoint sources of pollution include agricultural fields, cities, and
abandoned mines. Rainfall runs over the land and through the ground,
picking up pollutants such as herbicides, pesticides, and fertilizer from
agricultural fields and lawns; oil, antifreeze, car detergent, animal waste,
and road salt from urban areas; and acid and toxic elements from
abandoned mines. Then, this pollution is carried into surface water bodies
and groundwater. Nonpoint source pollution, which is the leading cause of
water pollution in the U.S., is usually much more difficult and expensive to
control than point source pollution because of its low concentration,
multiple sources, and much greater volume of water.
hte
pgs
ys vz
ae
A Commercial Meat Chicken Production House This chicken
factory farm is a possible major point source of water pollution.
Source: Larry Rana at Wikimedia Commons
Dry Weather
Spay
Outfall pipe and storm Wee
to river
Sewer to POTW
Combined Sewer System A combined sewer system is a possible
major point source of water pollution during heavy rain due to
overflow of untreated sewage. During dry weather (and small storms),
all flows are handled by the publicly owned treatment works (POTW).
During large storms, the relief structure allows some of the combined
stormwater and sewage to be discharged untreated to an adjacent water
body. Source: U.S. Environmental Protection Agency at Wikimedia
Commons
Types of Water Pollutants
Oxygen-demanding waste is an extremely important pollutant to
ecosystems. Most surface water in contact with the atmosphere has a small
amount of dissolved oxygen, which is needed by aquatic organisms for
cellular respiration. Bacteria decompose dead organic matter (chemically
represented in a simplified way as CH»O) and remove dissolved oxygen
(O>) according to the following reaction:
Equation:
CH,0 + O2 + CO, + H2O
Too much decaying organic matter in water is a pollutant because it
removes oxygen from water, which can kill fish, shellfish, and aquatic
insects. The amount of oxygen used by aerobic (in the presence of oxygen)
bacterial decomposition of organic matter is called biochemical oxygen
demand (BOD). The major source of dead organic matter in most natural
waters is sewage; grass and leaves are smaller sources. An unpolluted water
body with respect to oxygen is a turbulent river that flows through a natural
forest. Turbulence continually brings water in contact with the atmosphere
where the O> content is restored. The dissolved oxygen content in such a
river ranges from 10 to 14 ppm Op», BOD is low, and clean-water fish, e.g.,
bass, trout, and perch dominate. A polluted water body with respect to
oxygen is a stagnant deep lake in an urban setting with a combined sewer
system. This system favors a high input of dead organic carbon from
sewage overflows and limited chance for water circulation and contact with
the atmosphere. In such a lake, the dissolved O, content is <5 ppm Op,
BOD is high, and low O>-tolerant fish, e.g., carp and catfish dominate.
Excessive plant nutrients, particularly nitrogen (N) and phosphorous (P),
are pollutants closely related to oxygen-demanding waste. Aquatic plants
require about 15 nutrients for growth, most of which are plentiful in water.
N and P are called limiting nutrients, because they usually are present in
water at low concentrations and therefore restrict the total amount of plant
growth. This explains why N and P are major ingredients in most fertilizer.
High concentrations of N and P from human sources (mostly agricultural
and urban runoff including fertilizer, sewage, and P-based detergent) can
cause cultural eutrophication, which involves the rapid growth of aquatic
plants, particularly algae, called an algal bloom. Thick mats of floating and
rooted green or sometimes red algae ([link]) create water pollution, damage
the ecosystem by clogging fish gills and blocking sunlight, and damage lake
aesthetics by making recreation difficult and creating an eyesore. A small
percentage of algal species produce toxins that can kill fish, mammals, and
birds, and may cause human illness; explosive growths of these algae are
called harmful algal blooms ({link]). When the prolific algal layer dies, it
becomes oxygen-demanding waste, which can create very low O> water
(<~2 ppm O>), called hypoxia or dead zone because it causes death to
organisms that are unable to leave that environment. An estimated 50% of
lakes in North America, Europe, and Asia are negatively impacted by
cultural eutrophication. In addition, the size and number of marine hypoxic
zones have grown dramatically over the past 50 years ({link]), including a
very large dead zone located offshore Louisiana in the Gulf of Mexico.
Cultural eutrophication and hypoxia are difficult to combat, because they
are caused primarily by nonpoint source pollution, which is difficult to
regulate, and N and P, which are difficult to remove from wastewater.
Algal Bloom in River in Sichuan, China Algal
blooms can present problems for ecosystems and
human society. Source: Felix Andrews via Wikimedia
Commons
Harmful Algal Bloom Harmful algal bloom with deep red color.
Source: Kai Schumann via National Oceanic and Atmospheric
Administration
Particulate Organic Carbon pam Poputation Density (persoris/em')
S aaa
0 23 0 103 200 $00 1,000 ' 10 100 1,000 FOR 100K
Dead Zone Size (my)
nouns « ee
O1 4 10 100 1k 108
Aquatic Dead Zones Zones of hypoxia shown as red circles. Black
dots show hypoxia zones of unknown size, brown shading shows
population density, and blue shading shows density of particulate
organic carbon, an indicator of organic productivity. Source: Robert
Simmon & Jesse Allen at NASA Earth Observatory via Wikimedia
Commons
Pathogens are disease-causing microorganisms, e.g., viruses, bacteria,
parasitic worms, and protozoa, which cause a variety of intestinal diseases
such as dysentery, typhoid fever, hepatitis, and cholera. Pathogens are the
major cause of the water pollution crisis discussed at the beginning of this
section. Unfortunately nearly a billion people around the world are exposed
to waterborne pathogen pollution daily and around 1.5 million children
mainly in underdeveloped countries die every year of waterborne diseases
from pathogens. Pathogens enter water primarily from human and animal
fecal waste due to inadequate sewage treatment. In many underdeveloped
countries, sewage is discharged into local waters either untreated or after
only rudimentary treatment. In developed countries untreated sewage
discharge can occur from overflows of combined sewer systems, poorly
managed livestock factory farms, and leaky or broken sewage collection
systems. Water with pathogens can be remediated by adding chlorine or
ozone, by boiling, or by treating the sewage in the first place.
Oil spills are another kind of organic pollution. Oil spills can result from
supertanker accidents such as the Exxon Valdez in 1989, which spilled 10
million gallons of oil into the rich ecosystem of offshore south Alaska and
killed massive numbers of animals. The largest marine oil spill was the
Deepwater Horizon disaster, which began with a natural gas explosion (see
Figure [link]) at an oil well 65 km offshore of Louisiana and flowed for 3
months in 2010, releasing an estimated 200 million gallons of oil. The
worst oil spill ever occurred during the Persian Gulf war of 1991, when Iraq
deliberately dumped approximately 200 million gallons of oil in offshore
Kuwait and set more than 700 oil well fires that released enormous clouds
of smoke and acid rain for over nine months. During an oil spill on water,
oil floats to the surface because it is less dense than water, and the lightest
hydrocarbons evaporate, decreasing the size of the spill but polluting the air.
Then, bacteria begin to decompose the remaining oil, in a process that can
take many years. After several months only about 15% of the original
volume may remain, but it is in thick asphalt lumps, a form that is
particularly harmful to birds, fish, and shellfish. Cleanup operations can
include skimmer ships that vacuum oil from the water surface (effective
only for small spills), controlled burning (works only in early stages before
the light, ignitable part evaporates but also pollutes the air), dispersants
(detergents that break up oil to accelerate its decomposition, but some
dispersants may be toxic to the ecosystem), and bioremediation (adding
microorganisms that specialize in quickly decomposing oil, but this can
disrupt the natural ecosystem).
Deepwater Horizon Explosion Boats fighting the fire from an
explosion at the Deepwater Horizon drilling ng 1 in ee oe ioe
offshore Louisiana on April 20, 2010. Source: States Coast
suard via Wikimedia Commons
Toxic chemicals involve many different kinds and sources, primarily from
industry and mining. General kinds of toxic chemicals include hazardous
chemicals, which are a wide variety of synthetic organic and inorganic
chemicals such as acids, bases, cyanide, and a class of compounds called
persistent organic pollutants that includes DDT (pesticide), dioxin
(herbicide by-product), and PCBs (polychlorinated biphenyls, which were
used as a liquid insulator in electric transformers). Persistent organic
pollutants are long-lived in the environment, accumulate through the food
chain (bioaccumulation), and can be toxic. Another category of toxic
chemicals includes radioactive materials such as cesium, iodine, uranium,
and radon gas, which can result in long-term exposure to radioactivity if it
gets into the body. A final group of toxic chemicals is heavy metals such as
lead, mercury, arsenic, cadmium, and chromium, which can accumulate
through the food chain. Heavy metals are commonly produced by industry
and at metallic ore mines. Arsenic and mercury are discussed in more detail
below. The US EPA regulates 83 contaminants in drinking water to ensure a
safe public water supply. Similarly, at the international level the World
Health Organization has drinking water standards for a variety of
contaminants.
Arsenic (As) has been famous as an agent of death for many centuries. In
large doses arsenic causes cancer and can be fatal. Only recently have
scientists recognized that health problems can be caused by drinking small
arsenic concentrations in water over a long time. It attacks the central
nervous system and can damage the respiratory system, bladder, lungs,
liver, and kidneys. It enters the water supply naturally from weathering of
As-rich minerals and from human activities such as coal burning and
smelting of metallic ores. The worst case of arsenic poisoning occurred in
the densely populated impoverished country of Bangladesh, which had
experienced 100,000s of deaths from diarrhea and cholera each year from
drinking surface water contaminated with pathogens due to improper
sewage treatment. In the 1970s the United Nations provided aid for millions
of shallow water wells, which resulted in a dramatic drop in pathogenic
diseases. Unfortunately, many of the wells produced water naturally rich in
arsenic. Tragically, there are an estimated 77 million people (about half of
the population) who inadvertently may have been exposed to toxic levels of
arsenic in Bangladesh as a result. The World Health Organization has called
it the largest mass poisoning of a population in history.
Mercury (Hg) is used in a variety of electrical products, such as dry cell
batteries, fluorescent light bulbs, and switches, as well as in the
manufacture of paint, paper, vinyl chloride, and fungicides. In the
methylmercury form (CH3Hg’”) it is highly toxic; > 1 ppb of methylmercury
represents water contaminated with mercury. Mercury and other toxic
chemicals become concentrated in the food chain, especially in fish, in a
process caused biological magnification ([link]). It acts on the central
nervous system and can cause loss of sight, feeling, and hearing as well as
nervousness, shakiness, and death. Like arsenic, mercury enters the water
supply naturally from weathering of Hg-rich minerals and from human
activities such as coal burning and metal processing. A famous mercury
poisoning case in Minamata, Japan involved methylmercury-rich industrial
discharge that caused high Hg levels in fish. People in the local fishing
villages ate fish up to three times per day for over 30 years, which resulted
in over 2,000 deaths. During that time the responsible company and
national government did little to mitigate, help alleviate, or even
acknowledge the problem.
Biological magnification represents the processes in an ecosystem that
cause greater concentrations of a chemical, such as methylmercury, in
organisms higher up the food chain. Mercury and methylmercury are
present in only very small concentrations in seawater; however, at the base
of the food chain algae absorb methylmercury. Then, small fish eat the
algae, large fish and other organisms higher in the food chain eat the small
fish, and so on. Fish and other aquatic organisms absorb methylmercury
rapidly but eliminate it slowly from the body. Therefore, each step up the
food chain increases the concentration from the step below ((link]).
Largemouth bass can concentrate methylmercury up to 10 million times
over the water concentration and fish-eating birds can concentrate it even
higher. Other chemicals that exhibit biological magnification are DDT,
PCBs, and arsenic.
Biological
magnification
An illustrative
example of
biological
magnification
of mercury
from water
through the
food chain and
into a bird's
egg. Source:
U.S.
Geological
Survey
Other water pollutants include sediment and heat. Muddy water is bad for
drinking but even worse for underwater plants that need sunlight for
photosynthesis. Much of the sediment in water bodies is derived from the
erosion of soil, so it also represents a loss of agricultural productivity.
Thermal pollution involves the release of heated waters from power plants
and industry to surface water, causing a drop in the dissolved O> content,
which can stress fish.
Hard water contains abundant calcium and magnesium, which reduces its
ability to develop soapsuds and enhances scale (calcium and magnesium
carbonate minerals) formation on hot water equipment. Water softeners
remove calcium and magnesium, which allows the water to lather easily
and resist scale formation. Hard water develops naturally from the
dissolution of calcium and magnesium carbonate minerals in soil; it does
not have negative health effects in people.
Groundwater pollution can occur from underground sources and all of the
pollution sources that contaminate surface waters. Common sources of
groundwater pollution are leaking underground storage tanks for fuel, septic
tanks, agricultural activity, and landfills. Common groundwater pollutants
include nitrate, pesticides, volatile organic compounds, and petroleum
products. Polluted groundwater can be a more serious problem than
polluted surface water because the pollution in groundwater may go
undetected for a long time because usually it moves very slowly. As a
result, the pollution in groundwater may create a contaminant plume, a
large body of flowing polluted groundwater, making cleanup very costly.
By the time groundwater contamination is detected, the entity responsible
for the pollution may be bankrupt or nonexistent. Another troublesome
feature of groundwater pollution is that small amounts of certain pollutants,
e.g., petroleum products and organic solvents, can contaminate large areas.
In Denver, Colorado 80 liters of several organic solvents contaminated 4.5
trillion liters of groundwater and produced a 5 km long contaminant plume.
Most groundwater contamination occurs in shallow, unconfined aquifers
located near the contamination source. Confined aquifers are less
susceptible to pollution from the surface because of protection by the
confining layer. A major threat to groundwater quality is from underground
fuel storage tanks. Fuel tanks commonly are stored underground at gas
stations to reduce explosion hazards. Before 1988 in the U.S. these storage
tanks could be made of metal, which can corrode, leak, and quickly
contaminate local groundwater. Now, leak detectors are required and the
metal storage tanks are supposed to be protected from corrosion or replaced
with fiberglass tanks. Currently there are around 600,000 underground fuel
storage tanks in the U.S. and over 30% still do not comply with EPA
regulations regarding either release prevention or leak detection.
Contaminant Plume in Groundwater Mapping how a contaminant
plume will migrate once it reaches groundwater requires understanding
of the pollutant's chemical properties, local soil characteristics, and
how permeable the aquifer is. Source: United States Geological Survey
Sustainable Solutions to the Water Pollution Crisis?
Resolution of the global water pollution crisis described at the beginning of
this section requires multiple approaches to improve the quality of our fresh
water and move towards sustainability. The most deadly form of water
pollution, pathogenic microorganisms that cause waterborne diseases, kills
almost 2 million people in underdeveloped countries every year. The best
strategy for addressing this problem is proper sewage (wastewater)
treatment. Untreated sewage is not only a major cause of pathogenic
diseases, but also a major source of other pollutants, including oxygen-
demanding waste, plant nutrients (N and P), and toxic heavy metals.
Wastewater treatment is done at a sewage treatment plant in urban areas and
through a septic tank system in rural areas.
The main purpose of a sewage treatment plant is to remove organic matter
(oxygen-demanding waste) and kill bacteria; special methods also can be
used to remove plant nutrients and other pollutants. The numerous
processing steps at a conventional sewage treatment plant ([link]) include
pretreatment (screening and removal of sand and gravel), primary treatment
(settling or floatation to remove organic solids, fat, and grease), secondary
treatment (aerobic bacterial decomposition of organic solids), tertiary
treatment (bacterial decomposition of nutrients and filtration), disinfection
(treatment with chlorine, ozone, ultraviolet light, or bleach), and either
discharge to surface waters (usually a local river) or reuse for some other
purpose, such as irrigation, habitat preservation, and artificial groundwater
recharge. The concentrated organic solid produced during primary and
secondarytreatment is called sludge, which is treated in a variety of ways
including landfill disposal, incineration, use as fertilizer, and anaerobic
bacterial decomposition, which is done in the absence of oxygen. Anaerobic
decomposition of sludge produces methane gas, which can be used as an
energy source. To reduce water pollution problems, separate sewer systems
(where street runoff goes to rivers and only wastewater goes to a
wastewater treatment plant) are much better than combined sewer systems,
which can overflow and release untreated sewage into surface waters during
heavy rain. Some cities such as Chicago, Illinois have constructed large
underground caverns and also use abandoned rock quarries to hold storm
sewer overflow. After the rain stops, the stored water goes to the sewage
treatment plant for processing.
Steps at a Sewage Treatment Plant The numerous processing steps
at a conventional sewage treatment plant include pretreatment
(screening and removal of sand and gravel), primary treatment
(settling or floatation to remove organic solids, fat, and grease),
secondary treatment (aerobic bacterial decomposition of organic
solids), tertiary treatment (bacterial decomposition of nutrients and
filtration), disinfection (treatment with chlorine, ozone, ultraviolet
light, or bleach), and either discharge to surface waters (usually a local
river) or reuse for some other purpose, such as irrigation, habitat
preservation, and artificial groundwater recharge. Source: Leonard
G.via Wikipedia
A septic tank system is an individual sewage treatment system for homes in
rural and even some urban settings. The basic components of a septic tank
system ([link] include a sewer line from the house, a septic tank (a large
container where sludge settles to the bottom and microorganisms
decompose the organic solids anaerobically), and the drain field (network of
perforated pipes where the clarified water seeps into the soil and is further
purified by bacteria). Water pollution problems occur if the septic tank
malfunctions, which usually occurs when a system is established in the
wrong type of soil or maintained poorly.
SI udge PA Effluent
Sewage enters To drain field
from home and laterals
Septic System Septic tank system for
sewage treatment. Source: United
States Geological Survey
For many developing countries, financial aid is necessary to build adequate
sewage treatment facilities; however, the World Health Organization
estimates an estimated cost savings of between $3 and $34 for every $1
invested in clean water delivery and sanitation (Water for Life, 2005). The
cost savings are from health care savings, gains in work and school
productivity, and deaths prevented. Simple and inexpensive techniques for
treating water at home include chlorination, filters, and solar disinfection.
Another alternative is to use constructed wetlands technology (marshes
built to treat contaminated water), which is simpler and cheaper than a
conventional sewage treatment plant.
Bottled water is not a sustainable solution to the water crisis, despite
exponential growth in popularity in the U.S. and the world. Bottled water is
not necessarily any safer than the U.S. public water supply, it costs on
average about 700 times more than U.S. tap water, and every year it uses
approximately 200 billion plastic and glass bottles that have a relatively low
rate of recycling. Compared to tap water, it uses much more energy, mainly
in bottle manufacturing and long-distance transportation. If you don’t like
the taste of your tap water, then please use a water filter instead of bottled
water!
Additional sustainable solutions to the water pollution crisis include
legislation to eliminate or greatly reduce point sources of water pollution. In
the U.S., the Clean Water Act of 1972 and later amendments led to major
improvements in water quality ([link]). Nonpoint sources of water
pollution, e.g., agricultural runoff and urban runoff, are much harder to
regulate because of their widespread, diffuse nature. There are many
construction and agricultural practices that reduce polluted runoff including
no-till farming and sediment traps. Artificial aeration or mechanical mixing
can remediate lakes with oxygen depletion. Specific things that we can do
to reduce urban runoff include the following: keep soil, leaves, and grass
clippings off driveways, sidewalks, and streets; don't pour used motor oil,
antifreeze, paints, pesticides, or any household hazardous chemical down
the storm sewer or drain; recycle used motor oil; use hazardous waste
disposal programs offered by the community; compost your organic waste;
don't use fertilizers and herbicides on your lawn; and flush pet waste down
the toilet.
During the early 1900s rapid industrialization in the U.S. resulted in
widespread water pollution due to free discharge of waste into surface
waters. The Cuyahoga River in northeast Ohio caught fire numerous times
({link]), including a famous fire in 1969 that caught the nation’s attention.
In 1972 Congress passed one of the most important environmental laws in
U.S. history, the Federal Water Pollution Control Act, which is more
commonly called the Clean Water Act. The purpose of the Clean Water Act
and later amendments is to maintain and restore water quality, or in simpler
terms to make our water swimmable and fishable. It became illegal to dump
pollution into surface water unless there was formal permission and U.S.
water quality improved significantly as a result. More progress is needed
because currently the EPA considers over 40,000 U.S. water bodies as
impaired, most commonly due to pathogens, metals, plant nutrients, and
oxygen depletion. Another concern is protecting groundwater quality,
which is not yet addressed sufficiently by federal law.
Cuyahoga River on Fire Source: National Oceanic and
Atmospheric
Sometimes slow flow through a soil can naturally purify groundwater
because some pollutants, such as P, pesticides, and heavy metals,
chemically bind with surfaces of soil clays and iron oxides. Other pollutants
are not retained by soil particles: These include N, road salt, gasoline fuel,
the herbicide atrazine, tetrachloroethylene (a carcinogenic cleaning solvent
used in dry cleaning), and vinyl chloride. In other cases, slow groundwater
flow can allow bacteria to decompose dead organic matter and certain
pesticides. There are many other ways to remediate polluted groundwater.
Sometimes the best solution is to stop the pollution source and allow natural
cleanup. Specific treatment methods depend on the geology, hydrology, and
pollutant because some light contaminants flow on top of groundwater,
others dissolve and flow with groundwater, and dense contaminants can
sink below groundwater. A common cleanup method called pump and treat
involves pumping out the contaminated groundwater and treating it by
oxidation, filtration, or biological methods. Sometimes soil must be
excavated and sent to a landfill. In-situ treatment methods include adding
chemicals to immobilize heavy metals, creating a permeable reaction zone
with metallic iron that can destroy organic solvents, or using bioremediation
by adding oxygen or nutrients to stimulate growth of microorganisms.
References
Water for Life: Making it Happen (2005) World Health Organization and
UNICEF. Retrieved from
http://www.who.int/water_ sanitation health/waterforlife.pdf
World Health Statistics (2010) World Health Organization. Retrieved from
http://www.who.int/whosis/whostat/EN_WHS10_ Full .pdf
Introduction to Cells
Introduction
"The history of the knowledge of the phenomena of life and of the
organized world can be divided into two main periods. For a long time
anatomy, and particularly the anatomy of the human body, was the alpha
and omega of scientific knowledge. Further progress only became possible
with the discovery of the microscope. A long time had yet to pass until
through Schwann the cell was established as the final biological unit. It
would mean bringing coals to Newcastle were I to describe here the
immeasurable progress which biology, in all its branches, owes to the
introduction of this concept of the cell. For this concept is the axis around
which the whole of modern science revolves." Paul Ehrlich, "Partial Cell
Functions", Nobel Lecture, December 11, 1908
Ehrlich's enthusiasm for the cell is understandable. A single cell is the basic
unit of life, and the starting point for each and every human and other
organism on the planet. A cell is the smallest unit of a living thing. A living
thing, whether made of one cell (like bacteria) or many cells (like a human),
is called an organism. Thus, cells are the basic building blocks of all
organisms, and the study of cells is at the very heart of the research
enterprise that we call biological science.
Several cells of one kind that interconnect with each other and perform a
shared function form tissues, several tissues combine to form an organ
(your stomach, heart, or brain), and several organs make up an organ
system (such as the digestive system, circulatory system, or nervous
system). Several systems that function together form an organism (like a
human being). Here, we will examine the structure and function of cells.
There are many types of cells, all grouped into one of two broad categories:
prokaryotic and eukaryotic. For example, both animal and plant cells are
classified as eukaryotic cells, whereas bacterial cells are classified as
prokaryotic. Before discussing the criteria for determining whether a cell is
prokaryotic or eukaryotic, let’s first examine how biologists study cells.
Microscopy
Cells vary in size. With few exceptions, individual cells cannot be seen with
the naked eye, so scientists use microscopes (micro- = “small”; -scope = “to
look at”) to study them. A microscope is an instrument that magnifies an
object. Most photographs of cells are taken with a microscope, and these
images can also be called micrographs.
The optics of a microscope’s lenses change the orientation of the image that
the user sees. A specimen that is right-side up and facing right on the
microscope slide will appear upside-down and facing left when viewed
through a microscope, and vice versa. Similarly, if the slide is moved left
while looking through the microscope, it will appear to move right, and if
moved down, it will seem to move up. This occurs because microscopes use
two sets of lenses to magnify the image. Because of the manner by which
light travels through the lenses, this system of two lenses produces an
inverted image (binocular, or dissecting microscopes, work in a similar
manner, but include an additional magnification system that makes the final
image appear to be upright).
Light Microscopes
To give you a sense of cell size, a typical human red blood cell is about
eight millionths of a meter or eight micrometers (abbreviated as eight 1m,
or eight 1) in diameter; the head of a pin of is about two thousandths of a
meter (two mm) in diameter. That means about 250 red blood cells could fit
on the head of a pin.
Most student microscopes are classified as light microscopes ((link]a).
Visible light passes and is bent through the lens system to enable the user to
see the specimen. Light microscopes are advantageous for viewing living
organisms, but since individual cells are generally transparent, their
components are not distinguishable unless they are colored with special
stains. Staining, however, usually kills the cells.
Light microscopes commonly used in the undergraduate college laboratory
magnify up to approximately 400 times. Two parameters that are important
in microscopy are magnification and resolving power. Magnification is the
process of enlarging an object in appearance. Resolving power is the ability
of a microscope to distinguish two adjacent structures as separate: the
higher the resolution, the better the clarity and detail of the image. When oil
immersion lenses are used for the study of small objects, magnification is
usually increased to 1,000 times. In order to gain a better understanding of
cellular structure and function, scientists typically use electron microscopes.
(a) Most light microscopes used
in a college biology lab can
magnify cells up to
approximately 400 times and
have a resolution of about 200
nanometers. (b) Electron
microscopes provide a much
higher magnification, 100,000x,
and a have a resolution of 50
picometers. (credit a:
modification of work by
"GcG"/Wikimedia Commons;
credit b: modification of work
by Evan Bench)
Electron Microscopes
In contrast to light microscopes, electron microscopes ({link]|b) use a beam
of electrons instead of a beam of light. Not only does this allow for higher
magnification and, thus, more detail ([link]), it also provides higher
resolving power. The method used to prepare the specimen for viewing with
an electron microscope kills the specimen. Electrons have short
wavelengths (shorter than photons) that move best in a vacuum, so living
cells cannot be viewed with an electron microscope.
In a scanning electron microscope, a beam of electrons moves back and
forth across a cell’s surface, creating details of cell surface characteristics.
In a transmission electron microscope, the electron beam penetrates the cell
and provides details of a cell’s internal structures. As you might imagine,
electron microscopes are significantly more bulky and expensive than light
microscopes.
(a) These Salmonella bacteria appear as tiny
purple dots when viewed with a light
microscope. (b) This scanning electron
microscope micrograph shows Salmonella
bacteria (in red) invading human cells
(yellow). Even though subfigure (b) shows a
different Salmonella specimen than
subfigure (a), you can still observe the
comparative increase in magnification and
detail. (credit a: modification of work by
CDC/Armed Forces Institute of Pathology,
Charles N. Farmer, Rocky Mountain
Laboratories; credit b: modification of work
by NIAID, NIH; scale-bar data from Matt
Russell)
Cell Theory
The microscopes we use today are far more complex than those used in the
1600s by Antony van Leeuwenhoek, a Dutch shopkeeper who had great
skill in crafting lenses. Despite the limitations of his now-ancient lenses,
van Leeuwenhoek observed the movements of protista (a type of single-
celled organism) and sperm, which he collectively termed “animalcules.”
In a 1665 publication called Micrographia, experimental scientist Robert
Hooke coined the term “cell” for the box-like structures he observed when
viewing cork tissue through a lens. In the 1670s, van Leeuwenhoek
discovered bacteria and protozoa. Later advances in lenses, microscope
construction, and staining techniques enabled other scientists to see some
components inside cells.
By the late 1830s, botanist Matthias Schleiden and zoologist Theodor
Schwann were studying tissues and proposed the unified cell theory, which
States that all living things are composed of one or more cells, the cell is the
basic unit of life, and new cells arise from existing cells. Rudolf Virchow
later made important contributions to this theory.
Note:
Career Connection
Cytotechnologist
Have you ever heard of a medical test called a Pap smear ((link])? In this
test, a doctor takes a small sample of cells from the uterine cervix of a
patient and sends it to a medical lab where a cytotechnologist stains the
cells and examines them for any changes that could indicate cervical
cancer or a microbial infection.
Cytotechnologists (cyto- = “cell”) are professionals who study cells via
microscopic examinations and other laboratory tests. They are trained to
determine which cellular changes are within normal limits and which are
abnormal. Their focus is not limited to cervical cells; they study cellular
specimens that come from all organs. When they notice abnormalities, they
consult a pathologist, who is a medical doctor who can make a clinical
diagnosis.
Cytotechnologists play a vital role in saving people’s lives. When
abnormalities are discovered early, a patient’s treatment can begin sooner,
which usually increases the chances of a successful outcome.
“a
These uterine cervix cells, viewed
through a light microscope, were
obtained from a Pap smear.
Normal cells are on the left. The
cells on the right are infected with
human papillomavirus (HPV).
Notice that the infected cells are
larger; also, two of these cells
each have two nuclei instead of
one, the normal number. (credit:
modification of work by Ed
Uthman, MD; scale-bar data from
Matt Russell)
The Phylogenetic Relationship of Life
All of life can be grouped into three Domains Archaea, Bacteria and
Eukarya ({link]). Even though Archaea and Bacteria are prokaryotes, there
are enough differences between Archaea and Bacteria that warrant them
being in different Domains. Within the Domain Eukarya, there are at least
four Kingdoms Protists (multiple kingdoms), Fungi, Plantae and Animalia.
Figure 4 shows the current phylogentic tree of all these various groups that
we will be exploring.
Bacteria Archaea Eukarya
Animals
Fungi
Plants
Protista
The phylogenetic tree of the Domains Bacteria, Archeae
and the four Kingdoms of Eukarya. Work by Eva Horne
Our approach to Cell Biology
In this textbook, we explore cells and the chemistry of life in the reverse
order of many traditional textbooks. First, we explore the diversity of life at
the cellular level and then we investigate the chemistry of life or
Biochemistry. The reason why we take this approach is based on the fact
that many students have had some exposure to cells and this exposure
allows them to connect with the material. In addition, we feel a macro to
micro approach to investigating this material allows the learner the ability
to better connect how the biochemistry relates to the functioning cell.
Prokaryotic Cells
Introduction
"With the identification and characterization of the kingdoms we are for the
first time beginning to see the overall phylogenetic structure of the living
world. It is not structured in a bipartite way along the lines of the
organizationally dissimilar prokaryote and eukaryote. Rather, it is (at least)
tripartite, comprising (i) the typical bacteria, (ii) the line of descent
manifested in eukaryotic cytoplasms, and (iii) a little explored grouping,
represented so far only by methanogenic bacteria." Cal Woese and George
Fox, "Phylogenetic structure of the prokaryotic domain: the primary
kingdoms", Proceedings of the National Academy of Science, USA. 1977
74(11):5088-90.
Cells fall into one of two broad categories: prokaryotic and eukaryotic.
Until the publication of the paper cited above, it was believed that the
prokaryotic cells were all members of the group we know as Bacteria.
Woese and Fox (and others) laid out a strong case for another class of
prokaryotic cells, which they christened the Archaea. Cells of animals,
plants, fungi, and protists are all eukaryotes (eu- = “true”, karyo =
"nucleus") and are made up of eukaryotic cells. The single-celled organisms
of the domains Bacteria and Archaea are prokaryotes (pro- = “before”). We
will consider these two domains here, since they have some similarities, but
it is good to remember that Bacteria and Archea are as different from each
other as they are different from the Eukaryotes.
Components of Prokaryotic Cells
All cells share four common components: 1) a plasma membrane, an outer
covering that separates the cell’s interior from its surrounding environment;
2) cytoplasm, consisting of a jelly-like cytosol within the cell in which other
cellular components are found; 3) DNA, the genetic material of the cell; and
4) ribosomes, which synthesize proteins. However, prokaryotes differ from
eukaryotic cells in several ways.
A prokaryote is a simple, mostly single-celled (unicellular) organism that
lacks a nucleus, or any other membrane-bound organelle. We will shortly
come to see that this is significantly different in eukaryotes. Prokaryotic
DNA is found in a central part of the cell: the nucleoid ([link)).
Plasma
Flagellum
Chromosomal DNA is
localized in a region
called the nucleoid.
This figure shows the generalized
structure of a prokaryotic cell. All
prokaryotes have chromosomal DNA
localized in a nucleoid, ribosomes, a
plasma membrane, and a cell wall.
The other structures shown are present
in some, but not all, bacteria.
Most prokaryotes have a peptidoglycan cell wall and many have a
polysaccharide capsule ({link]). The cell wall acts as an extra layer of
protection, helps the cell maintain its shape, and prevents dehydration. The
capsule enables the cell to attach to surfaces in its environment. Some
prokaryotes have flagella, pili, or fimbriae. Flagella are used for
locomotion. Pili are used to exchange genetic material during a type of
reproduction called conjugation. Fimbriae are used by bacteria to attach to a
host cell.
Note:
Career Connection
Microbiologist
The most effective action anyone can take to prevent the spread of
contagious illnesses is to wash his or her hands. Why? Because microbes
(organisms so tiny that they can only be seen with microscopes) are
ubiquitous. They live on doorknobs, money, your hands, and many other
surfaces. If someone sneezes into his hand and touches a doorknob, and
afterwards you touch that same doorknob, the microbes from the sneezer’s
mucus are now on your hands. If you touch your hands to your mouth,
nose, or eyes, those microbes can enter your body and could make you
sick.
However, not all microbes (also called microorganisms) cause disease;
most are actually beneficial. You have microbes in your gut that make
vitamin K. Other microorganisms are used to ferment beer and wine.
Microbiologists are scientists who study microbes. Microbiologists can
pursue a number of careers. Not only do they work in the food industry,
they are also employed in the veterinary and medical fields. They can work
in the pharmaceutical sector, serving key roles in research and
development by identifying new sources of antibiotics that could be used
to treat bacterial infections.
Environmental microbiologists may look for new ways to use specially
selected or genetically engineered microbes for the removal of pollutants
from soil or groundwater, as well as hazardous elements from
contaminated sites. These uses of microbes are called bioremediation
technologies. Microbiologists can also work in the field of bioinformatics,
providing specialized knowledge and insight for the design, development,
and specificity of computer models of, for example, bacterial epidemics.
Cell Size
At 0.1 to 5.0 um in diameter, prokaryotic cells are significantly smaller than
eukaryotic cells, which have diameters ranging from 10 to 100 um ([Link)).
The small size of prokaryotes allows ions and organic molecules that enter
them to quickly diffuse to other parts of the cell. Similarly, any wastes
produced within a prokaryotic cell can quickly diffuse out. This is not the
case in eukaryotic cells, which have developed different structural
adaptations to enhance intracellular transport.
Animal
cell
Mitochondria
Protein
i)
Lipids Ostrich Adult
Bacteria egg female
0.1 nm inm 10 nm 100 nm tum 10 um 100 um 1mm 10 mm 100 mm 1m
Naked eye
td
Light microscope
Electron microscope
This figure shows relative sizes of microbes on a logarithmic scale
(recall that each unit of increase in a logarithmic scale represents a
10-fold increase in the quantity being measured).
Small size, in general, is necessary for all cells, whether prokaryotic or
eukaryotic. Let’s examine why that is so. First, we’ ll consider the area and
volume of a typical cell. Not all cells are spherical in shape, but most tend
to approximate a sphere. You may remember from your high school
geometry course that the formula for the surface area of a sphere is 4mr?,
while the formula for its volume is 4mr?/3. Thus, as the radius of a cell
increases, its surface area increases as the square of its radius, but its
volume increases as the cube of its radius (much more rapidly). Therefore,
as a Cell increases in size, its surface area-to-volume ratio decreases. This
same principle would apply if the cell had the shape of a cube ({link]). If the
cell grows too large, the plasma membrane will not have sufficient surface
area to support the rate of diffusion required for the increased volume. In
other words, as a cell grows, it becomes less efficient. One way to become
more efficient is to divide; another way is to develop organelles that
perform specific tasks. These adaptations lead to the development of more
sophisticated cells called eukaryotic cells.
Notice that as a cell increases in size,
its surface area-to-volume ratio
decreases. When there is insufficient
surface area to support a cell’s
increasing volume, a cell will either
divide or die. The cell on the left has a
volume of 1 mm? and a surface area
of 6 mm2, with a surface area-to-
volume ratio of 6 to 1, whereas the
cell on the right has a volume of 8
mm? and a surface area of 24 mm?,
with a surface area-to-volume ratio of
3 to 1.
Eukaryotic Cells
Introduction
"The cell, too, has a geography. And its reactions occur in a colloidal
apparatus, of which the form, and the catalytic activity of its manifold
surfaces, must efficiently contribute to the due guidance of chemical
reactions. " Frederick C. Hopkins, "Some Aspects of Biochemistry", The
Trish Journal of Medical Science, 1932, 79:344
Have you ever heard the phrase “form follows function?” It’s a philosophy
practiced in many industries. In architecture, this means that buildings
should be constructed to support the activities that will be carried out inside
them. For example, a skyscraper should be built with several elevator
banks; a hospital should be built so that its emergency room is easily
accessible.
Our natural world also utilizes the principle of form following function,
especially in cell biology, and this will become clear as we explore
eukaryotic cells ( [link]). Unlike prokaryotic cells, eukaryotic cells have: 1)
a membrane-bound nucleus; 2) numerous membrane-bound organelles
such as the endoplasmic reticulum, Golgi apparatus, chloroplasts,
mitochondria, and others; and 3) several, rod-shaped chromosomes. Of
these, Hopkins points out the membrane systems (the "manifold surfaces")
as being especially important. Indeed, the study of eukaryotic cells is in
many respects the study of the structure and function of these surfaces.
Different organelles have different forms and functions based on the form
and function of their component membranes. Indeed, the word “organelle”
means “little organ,” and organelles have specialized shapes and specialized
functions, just as the organs of your body have specialized shapes and
functions.
At this point, it should be clear to you that eukaryotic cells have a more
complex structure than prokaryotic cells. Organelles allow different
functions to be compartmentalized in different areas of the cell. Before
turning to organelles, let’s first examine two important components of the
cell: the plasma membrane and the cytoplasm.
These figures show the major organelles and other cell components of
(a) a typical animal cell and (b) a typical eukaryotic plant cell. The
plant cell has a cell wall, chloroplasts, plastids, and a central vacuole—
structures not found in animal cells. Plant cells do not have lysosomes
or centrosomes.
Nucleus Cytoskeleton
Nuclear envelope: Microtubules: form the
membrane enclosing | mitotic spindle and
the nucleus. Protein-lined maintain cell shape.
pores allow material to Centrosome: microtubule-
move in and out. organizing center.
Chromatin: DNA plus Intermediate filaments:
associated proteins. fibrous proteins that hold
Nucleolus: organelles in place.
condensed region Microfilaments:
where ribosomes fibrous proteins;
are formed. form the cellular
Peroxisome: PI
metabolizes peat
waste membrane
Lysosome:
digests food.
Golgi apparatus:
modifies proteins.
Endoplasmic I
: m
reticulum Cylopiss
Rough: associated
with ribosomes;
makes secretory and
membrane proteins.
Smooth: makes lipids.
Plasmodesmata: Endoplasmic reticulum Nucleus: contains
channels connect smooth rough chromatin and a
two plant cells nucleolus as in
an animal cell
Mitochondria:
produce energy.
Endosome
Cell wall: maintains
cell shape
Plasma
membrane
Cytoplasm
= Ribosomes
Central vacuole:
filled with cell sap
that maintains
pressure against
cell wall
Golgi
apparatus
Mitochondria
Cytoskeleton:
microtubules
intermediate
filaments Chloroplast: site Plastid: stores
microfilaments of photosynthesis pigments
Peroxisome
The Plasma Membrane
Like prokaryotes, eukaryotic cells have a plasma membrane ( [link]), a
phospholipid bilayer with embedded proteins that separates the internal
contents of the cell from its surrounding environment. A phospholipid is a
lipid molecule with two fatty acid chains and a phosphate-containing group.
The plasma membrane controls the passage of organic molecules, ions,
water, and oxygen into and out of the cell. Wastes (such as carbon dioxide
and ammonia) also leave the cell by passing through the plasma membrane.
Thus, the plasma membrane is said to be semi-permeable
Glycoprotein: protein with Glycolipid: lipid with
—. carbohydrate attached is carbohydrate
attached
Peripheral membrane Phospholipid
protein bilayer
Integral membrane Chotessarct Protein channel
protein
Filaments of the cytoskeleton
The eukaryotic plasma membrane is a phospholipid bilayer with
proteins and cholesterol embedded in it.
The plasma membranes of cells that specialize in absorption are folded into
fingerlike projections called microvilli (singular = microvillus); ( [link]).
Such cells are typically found lining the small intestine, the organ that
absorbs nutrients from digested food. This is an excellent example of form
following function. People with celiac disease have an immune response to
gluten, which is a protein found in wheat, barley, and rye. The immune
response damages microvilli, and thus, afflicted individuals cannot absorb
nutrients. This leads to malnutrition, cramping, and diarrhea. Patients
suffering from celiac disease must follow a gluten-free diet.
Microvilli
Side of
cell facing
inside of
small
intestine
Plasma membrane Nucleus
Microvilli, shown here as they appear on cells lining the small
intestine, increase the surface area available for absorption. These
microvilli are only found on the area of the plasma membrane that
faces the cavity from which substances will be absorbed. (credit
"micrograph": modification of work by Louisa Howard)
The Cytoplasm
The cytoplasm is the entire region of a cell between the plasma membrane
and the nuclear envelope (a structure to be discussed shortly). It is made up
of organelles suspended in the gel-like cytosol, the cytoskeleton, and
various chemicals ( [link]). Even though the cytoplasm consists of 70 to 80
percent water, it has a semi-solid consistency, which comes from the
proteins within it. However, proteins are not the only organic molecules
found in the cytoplasm. Glucose and other simple sugars, polysaccharides,
amino acids, nucleic acids, fatty acids, and derivatives of glycerol are found
there, too. Ions of sodium, potassium, calcium, and many other elements are
also dissolved in the cytoplasm. Many metabolic reactions, including
protein synthesis, take place in the cytoplasm.
The Nucleus
Typically, the nucleus is the most prominent organelle in a cell ( [link]). The
nucleus (plural = nuclei) houses the cell’s DNA and directs the synthesis of
ribosomes and proteins. Let’s look at it in more detail ( [link]).
Endoplasmic
reticulum
Nucleolus
Chromatin
Nucleoplasm
Nuclear pore
Nuclear envelope
The nucleus stores chromatin (DNA
plus proteins) in a gel-like substance
called the nucleoplasm. The nucleolus
is a condensed region of chromatin
where ribosome synthesis occurs. The
boundary of the nucleus is called the
nuclear envelope. It consists of two
phospholipid bilayers: an outer
membrane and an inner membrane.
The nuclear membrane is continuous
with the endoplasmic reticulum.
Nuclear pores allow substances to
enter and exit the nucleus.
The Nuclear Envelope
The nuclear envelope is a double-membrane structure that constitutes the
outermost portion of the nucleus ( [link]). Both the inner and outer
membranes of the nuclear envelope are phospholipid bilayers.
The nuclear envelope is punctuated with pores that control the passage of
ions, molecules, and RNA between the nucleoplasm and cytoplasm. The
nucleoplasm is the semi-solid fluid inside the nucleus, where we find the
chromatin and the nucleolus.
Chromatin and Chromosomes
To understand chromatin, it is helpful to first consider chromosomes.
Chromosomes are structures within the nucleus that are made up of DNA,
the hereditary material. You may remember that in prokaryotes, DNA is
organized into a single circular chromosome. In eukaryotes, chromosomes
are linear structures. Every eukaryotic species has a specific number of
chromosomes in the nuclei of its body’s cells. For example, in humans, the
chromosome number is 46, while in fruit flies, it is eight. Chromosomes are
only visible and distinguishable from one another when the cell is getting
ready to divide. When the cell is in the growth and maintenance phases of
its life cycle, proteins are attached to chromosomes, and they resemble an
unwound, jumbled bunch of threads. These unwound protein-chromosome
complexes are called chromatin ( [link]); chromatin describes the material
that makes up the chromosomes both when condensed and decondensed.
Zz 3
\
aT
Histone: a protein associated
with DNA
(a) This image shows various levels of the
organization of chromatin (DNA and protein). (b)
This image shows paired chromosomes. (credit b:
modification of work by NIH; scale-bar data from
Matt Russell)
The Nucleolus
We already know that the nucleus directs the synthesis of ribosomes, but
how does it do this? Some chromosomes have sections of DNA that encode
ribosomal RNA. A darkly staining area within the nucleus called the
nucleolus (plural = nucleoli) aggregates the ribosomal RNA with associated
proteins to assemble the ribosomal subunits that are then transported out
through the pores in the nuclear envelope to the cytoplasm.
Ribosomes
Ribosomes are the cellular organelles responsible for protein synthesis.
When viewed through an electron microscope, ribosomes appear either as
clusters (polyribosomes) or single, tiny dots that float freely in the
cytoplasm. They may be attached to the cytoplasmic side of the plasma
membrane or the cytoplasmic side of the endoplasmic reticulum and the
outer membrane of the nuclear envelope ( [link]). Electron microscopy has
shown us that ribosomes, which are large complexes of protein and RNA,
consist of two subunits, aptly called large and small ( [link]). Ribosomes
receive their “orders” for protein synthesis from the nucleus where the
DNA is transcribed into messenger RNA (mRNA). The mRNA travels to
the ribosomes, which translate the code provided by the sequence of the
nitrogenous bases in the mRNA into a specific order of amino acids ina
protein. Amino acids are the building blocks of proteins.
Growing peptide
chain
Ribosome
large
subunit
tRNA
Ribosome
small
subunit
Ribosomes are made up of a large
subunit (top) and a small subunit
(bottom). During protein synthesis,
ribosomes assemble amino acids into
proteins.
Because proteins synthesis is an essential function of all cells (including
enzymes, hormones, antibodies, pigments, structural components, and
surface receptors), ribosomes are found in practically every cell. Ribosomes
are particularly abundant in cells that synthesize large amounts of protein.
For example, the pancreas is responsible for creating several digestive
enzymes and the cells that produce these enzymes contain many ribosomes.
Thus, we see another example of form following function.
Mitochondria
Mitochondria (singular = mitochondrion) are often called the
“powerhouses” or “energy factories” of a cell because they are responsible
for making adenosine triphosphate (ATP), the cell’s main energy-carrying
molecule. ATP represents the short-term stored energy of the cell. Cellular
respiration is the process of making ATP using the chemical energy found
in glucose and other nutrients. In mitochondria, this process uses oxygen
and produces carbon dioxide as a waste product. In fact, the carbon dioxide
that you exhale with every breath comes from the cellular reactions that
produce carbon dioxide as a byproduct.
In keeping with our theme of form following function, it is important to
point out that muscle cells have a very high concentration of mitochondria
that produce ATP. Your muscle cells need a lot of energy to keep your body
moving. When your cells don’t get enough oxygen, they do not make a lot
of ATP. Instead, the small amount of ATP they make in the absence of
oxygen is accompanied by the production of lactic acid.
Mitochondria are oval-shaped, double membrane organelles ( [link]) that
have their own ribosomes and DNA. Each membrane is a phospholipid
bilayer embedded with proteins. The inner layer has folds called cristae.
The area surrounded by the folds is called the mitochondrial matrix. The
cristae and the matrix have different roles in cellular respiration.
Mitochondrial
matrix
Cristae
Outer membrane
Inner membrane
This electron micrograph shows a
mitochondrion as viewed with a
transmission electron microscope.
This organelle has an outer membrane
and an inner membrane. The inner
membrane contains folds, called
cristae, which increase its surface
area. The space between the two
membranes is called the
intermembrane space, and the space
inside the inner membrane is called
the mitochondrial matrix. ATP
synthesis takes place on the inner
membrane. (credit: modification of
work by Matthew Britton; scale-bar
data from Matt Russell)
Peroxisomes
Peroxisomes are small, round organelles enclosed by single membranes.
They carry out oxidation reactions that break down fatty acids and amino
acids. They also detoxify many poisons that may enter the body. (Many of
these oxidation reactions release hydrogen peroxide, H»O>, which would be
damaging to cells; however, when these reactions are confined to
peroxisomes, enzymes safely break down the H»O> into oxygen and water.)
For example, alcohol is detoxified by peroxisomes in liver cells.
Glyoxysomes, which are specialized peroxisomes in plants, are responsible
for converting stored fats into sugars.
Vesicles and Endosomes
Vesicles and endosomes are membrane-bound sacs that function in storage
and transport. Other than the fact that vacuoles are somewhat larger than
vesicles, there is a very subtle distinction between them: The membranes of
vesicles can fuse with either the plasma membrane or other membrane
systems within the cell. Additionally, some agents such as enzymes within
plant vacuoles break down macromolecules. The membrane of a vacuole
does not fuse with the membranes of other cellular components.
Animal Cells versus Plant Cells
At this point, you know that each eukaryotic cell has a plasma membrane,
cytoplasm, a nucleus, ribosomes, mitochondria, peroxisomes, and in some,
vacuoles, but there are some striking differences between animal and plant
cells. While both animal and plant cells have microtubule organizing
centers (MTOCs), animal cells also have centrioles associated with the
MTOC: a complex called the centrosome. Animal cells each have a
centrosome and lysosomes, whereas plant cells do not. Plant cells have a
cell wall, chloroplasts and other specialized plastids, and a large central
vacuole, whereas animal cells do not.
The Centrosome
The centrosome is a microtubule-organizing center found near the nuclei of
animal cells. It contains a pair of centrioles, two structures that lie
perpendicular to each other ( [link]). Each centriole is a cylinder of nine
triplets of microtubules.
Centriole
Microtubule
triplet
Centriole
The centrosome consists of two
centrioles that lie at right angles to
each other. Each centriole is a cylinder
made up of nine triplets of
microtubules. Nontubulin proteins
(indicated by the green lines) hold the
microtubule triplets together.
The centrosome (the organelle where all microtubules originate) replicates
itself before a cell divides, and the centrioles appear to have some role in
pulling the duplicated chromosomes to opposite ends of the dividing cell.
However, the exact function of the centrioles in cell division isn’t clear,
because cells that have had the centrosome removed can still divide, and
plant cells, which lack centrosomes, are capable of cell division.
Lysosomes
Another set of organelles only found in eukaryotes are lysosomes. The
lysosomes are the cell’s “garbage disposal.” Enzymes within the lysosomes
aid the breakdown of proteins, polysaccharides, lipids, nucleic acids, and
even worn-out organelles. These enzymes are active at a much lower pH
than that of the cytoplasm. Therefore, the pH within lysosomes is more
acidic than the pH of the cytoplasm. Many reactions that take place in the
cytoplasm could not occur at a low pH, so again, the advantage of
compartmentalizing the eukaryotic cell into organelles is apparent.
The Cell Wall
If you examine [link]b, the diagram of a plant cell, you will see a structure
external to the plasma membrane called the cell wall. The cell wall is a
rigid covering that protects the cell, provides structural support, and gives
shape to the cell. Fungal and protistan cells also have cell walls. While the
chief component of prokaryotic cell walls is peptidoglycan, the major
organic molecule in the plant cell wall is cellulose ( [link]), a
polysaccharide made up of glucose units. Have you ever noticed that when
you bite into a raw vegetable, like celery, it crunches? That’s because you
are tearing the rigid cell walls of the celery cells with your teeth.
H,C — OH H,C — OH
OH H OH H OH H
oO OH H OH H
HC — OH H,C — OH H.C — OH
Cellulose is a long chain of B-glucose
molecules connected by a 1-4 linkage.
The dashed lines at each end of the
figure indicate a series of many more
glucose units. The size of the page
makes it impossible to portray an
entire cellulose molecule.
Chloroplasts
Like the mitochondria, chloroplasts have their own DNA and ribosomes,
but chloroplasts have an entirely different function. Chloroplasts are plant
cell organelles that carry out photosynthesis. Photosynthesis is the series of
reactions that use carbon dioxide, water, and light energy to make glucose
and oxygen. This is a major difference between plants and animals; plants
(autotrophs) are able to make their own food, like sugars, while animals
(heterotrophs) must ingest their food.
Like mitochondria, chloroplasts have outer and inner membranes, but
within the space enclosed by a chloroplast’s inner membrane is a set of
interconnected and stacked fluid-filled membrane sacs called thylakoids (
[link]). Each stack of thylakoids is called a granum (plural = grana). The
fluid enclosed by the inner membrane that surrounds the grana is called the
stroma.
Outer Intermembrane Inner Stroma
membrane space membrane (aqueous fluid)
Thylakoid
Granum
(stack of thylakoids)
The chloroplast has an outer
membrane, an inner membrane, and
membrane structures called thylakoids
that are stacked into grana. The space
inside the thylakoid membranes is
called the thylakoid space. The light
harvesting reactions take place in the
thylakoid membranes, and the
synthesis of sugar takes place in the
fluid inside the inner membrane,
which is called the stroma.
Chloroplasts also have their own
genome, which is contained on a
single circular chromosome.
The chloroplasts contain a green pigment called chlorophyll, which
captures the light energy that drives the reactions of photosynthesis. Like
plant cells, photosynthetic protists also have chloroplasts. Some bacteria
perform photosynthesis, but their chlorophyll is not relegated to an
organelle.
The Central Vacuole
Previously, we mentioned vacuoles as essential components of plant cells.
If you look at [link]b, you will see that plant cells each have a large central
vacuole that occupies most of the area of the cell. The central vacuole
plays a key role in regulating the cell’s concentration of water in changing
environmental conditions. Have you ever noticed that if you forget to water
a plant for a few days, it wilts? That’s because as the water concentration in
the soil becomes lower than the water concentration in the plant, water
moves out of the central vacuoles and cytoplasm. As the central vacuole
shrinks, it leaves the cell wall unsupported. This loss of support to the cell
walls of plant cells results in the wilted appearance of the plant.
The central vacuole also supports the expansion of the cell. When the
central vacuole holds more water, the cell gets larger without having to
invest a lot of energy in synthesizing new cytoplasm.
Protists
Introduction
"The 31th of May, I perceived in the same water more of those Animals, as
also some that were somewhat bigger. And I imagine that ten hundred
thousand of these little Creatures do not equal an ordinary grain of Sand in
bigness..." Antoni von Leeuwenhoek, Letter to H. Oldenburg, 9 October
1676
Von Leeuwenhoek's amazement at seeing protists for the first time is
understandable. These tiny creatures are abundant, diverse, and fit into
many biological niches. There are over 100,000 described living species of
protists, and it is unclear how many undescribed species may exist. Since
many protists live as commensals or parasites in other organisms and these
relationships are often species-specific, there is a huge potential for protist
diversity that matches the diversity of hosts. As the catchall term for
eukaryotic organisms that are not animal, plant, or fungi, it is not surprising
that very few characteristics are common to all protists. Since Protista is a
catchall group of organisms, Biologists are now investigating the
evolutionary relationships of this groups and are formulating many new
Kingdoms within the group of Protists.
Cell Structure
The cells of protists are among the most elaborate of all cells. Most protists
are microscopic and unicellular, but some true multicellular forms exist. A
few protists live as colonies that behave in some ways as a group of free-
living cells and in other ways as a multicellular organism. Still other protists
are composed of enormous, multinucleate, single cells that look like
amorphous blobs of slime, or in other cases, like ferns. In fact, many protist
cells are multinucleated; in some species, the nuclei are different sizes and
have distinct roles in protist cell function.
Single protist cells range in size from less than a micrometer to three meters
in length to hectares. Protist cells may be enveloped by animal-like plasma
membranes or plant-like cell walls. Others are encased in glassy silica-
based shells or wound with pellicles of interlocking protein strips. The
pellicle functions like a flexible coat of armor, preventing the protist from
being torn or pierced without compromising its range of motion.
Metabolism
Protists exhibit many forms of nutrition and may be aerobic or anaerobic.
Protists that store energy by photosynthesis belong to a group of
photoautotrophs and are characterized by the presence of chloroplasts.
Other protists are heterotrophic and consume organic materials (such as
other organisms) to obtain nutrition. Amoebas and some other heterotrophic
protist species ingest particles by a process called phagocytosis, in which
the plasma membrane engulfs a food particle and brings it inward, pinching
off an intracellular membranous sac, or vesicle, called a food vacuole
({link]). The vesicle containing the ingested particle, the phagosome, then
fuses with a lysosome containing hydrolytic enzymes to produce a
phagolysosome, and the food particle is broken down into small molecules
that can diffuse into the cytoplasm and be used in cellular metabolism.
Undigested remains ultimately are expelled from the cell via exocytosis.
Phagocytosis
Food particle | Food vacuole Exocytic vesicle containing
undigested material
Pseudopods
Lysosome containing ~
digestive enzymes
The stages of phagocytosis
include the engulfment of a
food particle, the digestion of
the particle using hydrolytic
enzymes contained within a
lysosome, and the expulsion of
undigested materials from the
cell.
Subtypes of heterotrophs, called saprobes, absorb nutrients from dead
organisms or their organic wastes. Some protists can function as
mixotrophs, obtaining nutrition by photoautotrophic or heterotrophic
routes, depending on whether sunlight or organic nutrients are available.
Motility
The majority of protists are motile, but different types of protists have
evolved varied modes of movement ([link]). Some protists have one or
more flagella, which they rotate or whip. Others are covered in rows or tufts
of tiny cilia that they coordinately beat to swim. Still others form
cytoplasmic extensions called pseudopodia anywhere on the cell, anchor the
pseudopodia to a substrate, and pull themselves forward. Some protists can
move toward or away from a stimulus, a movement referred to as taxis.
Movement toward light, termed phototaxis, is accomplished by coupling
their locomotion strategy with a light-sensing organ.
Paramecium Amoeba Euglena
Pseudopod Flagellum
(a) (b) (c)
Protists use various methods for transportation. (a)
Paramecium waves hair-like appendages called cilia to
propel itself. (b) Amoeba uses lobe-like pseudopodia to
anchor itself to a solid surface and pull itself forward. (c)
Euglena uses a whip-like tail called a flagellum to propel
itself.
Life Cycles
Protists reproduce by a variety of mechanisms. Most undergo some form of
asexual reproduction, such as binary fission, to produce two daughter cells.
In protists, binary fission can be divided into transverse or longitudinal,
depending on the axis of orientation; sometimes Paramecium exhibits this
method. Some protists such as the true slime molds exhibit multiple fission
and simultaneously divide into many daughter cells. Others produce tiny
buds that go on to divide and grow to the size of the parental protist. Sexual
reproduction, involving meiosis and fertilization, is common among
protists, and many protist species can switch from asexual to sexual
reproduction when necessary. Sexual reproduction is often associated with
periods when nutrients are depleted or environmental changes occur. Sexual
reproduction may allow the protist to recombine genes and produce new
variations of progeny that may be better suited to surviving in the new
environment. However, sexual reproduction is often associated with
resistant cysts that are a protective, resting stage. Depending on their
habitat, the cysts may be particularly resistant to temperature extremes,
desiccation, or low pH. This strategy also allows certain protists to “wait
out” stressors until their environment becomes more favorable for survival
or until they are carried (such as by wind, water, or transport on a larger
organism) to a different environment, because cysts exhibit virtually no
cellular metabolism.
Protist life cycles range from simple to extremely elaborate. Certain
parasitic protists have complicated life cycles and must infect different host
species at different developmental stages to complete their life cycle. Some
protists are unicellular in the haploid form and multicellular in the diploid
form, a strategy employed by animals. Other protists have multicellular
stages in both haploid and diploid forms, a strategy called alternation of
generations that is also used by plants.
Habitats
Nearly all protists exist in some type of aquatic environment, including
freshwater and marine environments, damp soil, and even snow. Several
protist species are parasites that infect animals or plants. A few protist
species live on dead organisms or their wastes, and contribute to their
decay.
Fungi
Introduction
"When brewer's yeast is mixed with water the microscope reveals that the
yeast dissolves into endless small balls, which are scarcely 1/800th of a line
in diameter... If these small balls are placed in sugar water, it can be seen
that they consist of the eggs of animals. As they expand, they burst, and
from them develop small creatures that multiply with unbelievable rapidity
in a most unheard-of way." Friedrich Wohler, Annalen der Pharmacie und
Chemie, 29:100-104, 1839
WoOhler's fanciful depiction of yeast as tiny animals, while not reflecting
current taxonomic opinions, is understandable. Yeast, a single-celled
member of the Kingdom Fungi, share many characteristics with animals,
include being heterotrophic. But they also have cell walls, a characteristic
that they share with plants. But even though a superficial glance might
indicate that Fungi occupy the middle ground between animals and plants,
they are unique in several ways, and have many interesting and useful
metabolites and products (such as penicillin, or ethanol). So let's briefly
introduce the Fungi here, and return to them in a later module for a more
detailed look at these mysterious creatures.
(a) (b) (c)
The (a) familiar mushroom is only one type of fungus. The
brightly colored fruiting bodies of this (b) coral fungus are
displayed. This (c) electron micrograph shows the spore-
bearing structures of Aspergillus, a type of toxic fungi
found mostly in soil and plants. (credit a: modification of
work by Chris Wee; credit b: modification of work by Cory
Zanker; credit c: modification of work by Janice Haney
Carr, Robert Simmons, CDC; scale-bar data from Matt
Russell)
The word fungus comes from the Latin word for mushroom. Indeed, the
familiar mushrooms are fungi, but there are many other types of fungi as
well ((link]). The kingdom Fungi includes an enormous variety of living
organisms collectively referred to as Eumycota, or true fungi. While
scientists have identified about 100,000 species of fungi, this is only a
fraction of the over 1 million species likely present on Earth. Edible
mushrooms, yeasts, black mold, and Penicillium notatum (the producer of
the antibiotic penicillin) are all members of the kingdom Fungi, which
belongs to the domain Eukarya. As eukaryotes, a typical fungal cell
contains a true nucleus and many membrane-bound organelles.
Fungi were once considered plant-like organisms; however, DNA
comparisons have shown that fungi are more closely related to animals than
plants. Fungi are not capable of photosynthesis: They use complex organic
compounds as sources of energy and carbon. Some fungal organisms
multiply only asexually, whereas others undergo both asexual reproduction
and sexual reproduction. Most fungi produce a large number of spores that
are disseminated by the wind. Like bacteria, fungi play an essential role in
ecosystems, because they are decomposers and participate in the cycling of
nutrients by breaking down organic materials into simple molecules.
Fungi often interact with other organisms, forming mutually beneficial or
mutualistic associations. Fungi also cause serious infections in plants and
animals. For example, Dutch elm disease is a particularly devastating
fungal infection that destroys many native species of elm (Ulmus spp.). The
fungus infects the vascular system of the tree. It was accidentally
introduced to North America in the 1900s and decimated elm trees across
the continent. Dutch elm disease is caused by the fungus Ophiostoma ulmi.
The elm bark beetle acts as a vector and transmits the disease from tree to
tree. Many European and Asiatic elms are less susceptible than American
elms.
In humans, fungal infections are generally considered challenging to treat
because, unlike bacteria, they do not respond to traditional antibiotic
therapy since they are also eukaryotes. These infections may prove deadly
for individuals with a compromised immune system.
Fungi have many commercial applications. The food industry uses yeasts in
baking, brewing, and wine making. Many industrial compounds are
byproducts of fungal fermentation. Fungi are the source of many
commercial enzymes and antibiotics.
Cell Structure and Function
Fungi are eukaryotes and as such have a complex cellular organization
({link]). As eukaryotes, fungal cells contain a membrane-bound nucleus. A
few types of fungi have structures comparable to the plasmids (loops of
DNA) seen in bacteria. Fungal cells also contain mitochondria and a
complex system of internal membranes, including the endoplasmic
reticulum and Golgi apparatus.
Fungal cells do not have chloroplasts. Although the photosynthetic pigment
chlorophyll is absent, many fungi display bright colors, ranging from red to
green to black. The poisonous Amanita muscaria (fly agaric) is
recognizable by its bright red cap with white patches. Other fungi can be
red, or purple, or blue, although many are simply white or brownish.
Pigments in fungi are associated with the cell wall and play a protective role
against ultraviolet radiation. Some pigments are toxic.
A. Fungal Hyphae B. Cellular components of
a fungal hypha
Fungal Hyphae. A - Diagram of a branching hyphal mass. B - Diagram
of the cellular components of the tip of one of the hyphae. 1- Cell wall
2- Septum 3- Mitochondrion 4- Vacuole 5- Ergosterol crystal 6-
Ribosome 7- Nucleus 8- Endoplasmic reticulum 9- Lipid body 10-
Plasma membrane 11- Growth tip and vesicles 12- Golgi apparatus.
(From Creative Commons, original artist - AHiggins12)
Like plant cells, fungal cells are surrounded by a thick cell wall; however,
the rigid layers contain the complex polysaccharides chitin and glucan.
Cellulose, the main component of plant cell walls, is found rarely in fungi.
Chitin, also found in the exoskeleton of insects, gives structural strength to
the cell walls of fungi. The cell wall protects the cell from desiccation and
predators. Fungi have plasma membranes similar to other eukaryotes,
except that the structure is stabilized by ergosterol, a steroid molecule that
functions like the cholesterol found in animal plasma membranes. Most
members of the kingdom Fungi are nonmotile. Flagella are produced only
by the gametes in the primitive division Chytridiomycota.
Eukaryotic Origins
Introduction
"In most of the animals we think we know best (mammals, reptiles,
insects), the genomes that determine limbs, eyes, and nervous systems, for
example, are very similar to our own. These animals, like us, are doubly
genomic. Even some unicellular beings that do not have eyes, limbs, or
nervous systems--such as amoebas and paramecia--contain both nuclear and
mitochondrial genomes. Plants and algae have these double genomes as
well, plus a third genome, of symbiotic origin. During their evolutionary
history, they ingested (but did not digest) photosynthetic blue-green
bacteria. Therefore, all visible photosynthetic organisms have at least three
genomes. But many organisms--such as the protists that inhabit termites--
contain within them up to five or more genomes." Lynn Margulis and
Dorion Sagan, "The Beast with Five Genomes", Natural History Vol. 110
Issue 5, p. 38, 2001
Living things fall into three large groups: Archaea, Bacteria, and Eukarya.
The first two have prokaryotic cells, and the third contains all eukaryotes.
But, as noted above, eukaryotes contain multiple genomes, and those
genomes indicate that eukaryotes probably arose by when one ancestor
"captured" another. A relatively sparse fossil record is available to help
discern what the first members of each of these lineages looked like, so it is
possible that all the events that led to the last common ancestor of extant
eukaryotes will never be clarified by the fossil record. However,
comparative biology of extant organisms, genomic analysis, and the limited
fossil record provide some insight into the history of Eukarya.
The earliest fossils found appear to be Bacteria, most likely cyanobacteria.
They are about 3.5 billion years old and are recognizable because of their
relatively complex structure and, for prokaryotes, relatively large cells.
Most other prokaryotes have small cells, 1 or 2 ym in size, and would be
difficult to pick out as fossils. Most living eukaryotes have cells measuring
10 pm or greater. Structures this size, which might be fossils, appear in the
geological record about 2.1 billion years ago.
Characteristics of Eukaryotes
Data from these fossils have led comparative biologists to the conclusion
that living eukaryotes are all descendants of a single common ancestor.
Mapping the characteristics found in all major groups of eukaryotes reveals
that the following characteristics must have been present in the last
common ancestor, because these characteristics are present in at least some
of the members of each major lineage.
iL,
Cells with nuclei surrounded by a nuclear envelope with nuclear pores.
This is the single characteristic that is both necessary and sufficient to
define an organism as a eukaryote. All extant eukaryotes have cells
with nuclei.
. Mitochondria. Some extant eukaryotes have very reduced remnants of
mitochondria in their cells, whereas other members of their lineages
have “typical” mitochondria.
. A cytoskeleton containing the structural and motility components
called actin microfilaments and microtubules. All extant eukaryotes
have these cytoskeletal elements.
. Flagella and cilia, organelles associated with cell motility. Some extant
eukaryotes lack flagella and/or cilia, but they are descended from
ancestors that possessed them.
. Chromosomes, each consisting of a linear DNA molecule coiled
around basic (alkaline) proteins called histones. The few eukaryotes
with chromosomes lacking histones clearly evolved from ancestors
that had them.
. Mitosis, a process of nuclear division wherein replicated chromosomes
are divided and separated using elements of the cytoskeleton. Mitosis
is universally present in eukaryotes.
. Sex, a process of genetic recombination unique to eukaryotes in which
diploid nuclei at one stage of the life cycle undergo meiosis to yield
haploid nuclei and subsequent karyogamy, a stage where two haploid
nuclei fuse together to create a diploid zygote nucleus.
. Members of all major lineages have cell walls, and it might be
reasonable to conclude that the last common ancestor could make cell
walls during some stage of its life cycle. However, not enough is
known about eukaryotes’ cell walls and their development to know
how much homology exists among them. If the last common ancestor
could make cell walls, it is clear that this ability must have been lost in
many groups.
Endosymbiosis and the Evolution of Eukaryotes
In order to understand eukaryotic organisms fully, it is necessary to
understand that all extant eukaryotes are descendants of a chimeric
organism that was a composite of a host cell and the cell(s) of an alpha-
proteobacterium that “took up residence” inside it. This major theme in the
origin of eukaryotes is known as endosymbiosis, one cell engulfing another
such that the engulfed cell survives and both cells benefit. Over many
generations, a symbiotic relationship can result in two organisms that
depend on each other so completely that neither could survive on its own.
Endosymbiotic events likely contributed to the origin of the last common
ancestor of today’s eukaryotes and to later diversification in certain lineages
of eukaryotes ({link]). Before explaining this further, it is necessary to
consider metabolism in prokaryotes.
Prokaryotic Metabolism
Many important metabolic processes arose in prokaryotes, and some of
these, such as nitrogen fixation, are never found in eukaryotes. The process
of aerobic respiration is found in all major lineages of eukaryotes, and it is
localized in the mitochondria. Aerobic respiration is also found in many
lineages of prokaryotes, but it is not present in all of them, and many forms
of evidence suggest that such anaerobic prokaryotes never carried out
aerobic respiration nor did their ancestors.
While today’s atmosphere is about one-fifth molecular oxygen (O>),
geological evidence shows that it originally lacked Oy. Without oxygen,
aerobic respiration would not be expected, and living things would have
relied on fermentation instead. At some point before, about 3.5 billion years
ago, some prokaryotes began using energy from sunlight to power anabolic
processes that reduce carbon dioxide to form organic compounds. That is,
they evolved the ability to photosynthesize. Hydrogen, derived from various
sources, was captured using light-powered reactions to reduce fixed carbon
dioxide in the Calvin cycle. The group of Gram-negative bacteria that gave
rise to cyanobacteria used water as the hydrogen source and released O» as
a waste product.
Eventually, the amount of photosynthetic oxygen built up in some
environments to levels that posed a risk to living organisms, since it can
damage many organic compounds. Various metabolic processes evolved
that protected organisms from oxygen, one of which, aerobic respiration,
also generated high levels of ATP. It became widely present among
prokaryotes, including in a group we now call alpha-proteobacteria.
Organisms that did not acquire aerobic respiration had to remain in oxygen-
free environments. Originally, oxygen-rich environments were likely
localized around places where cyanobacteria were active, but by about 2
billion years ago, geological evidence shows that oxygen was building up to
higher concentrations in the atmosphere. Oxygen levels similar to today’s
levels only arose within the last 700 million years.
Recall that the first fossils that we believe to be eukaryotes date to about 2
billion years old, so they appeared as oxygen levels were increasing. Also,
recall that all extant eukaryotes descended from an ancestor with
mitochondria. These organelles were first observed by light microscopists
in the late 1800s, where they appeared to be somewhat worm-shaped
structures that seemed to be moving around in the cell. Some early
observers suggested that they might be bacteria living inside host cells, but
these hypotheses remained unknown or rejected in most scientific
communities.
Endosymbiotic Theory
As cell biology developed in the twentieth century, it became clear that
mitochondria were the organelles responsible for producing ATP using
aerobic respiration. In the 1960s, American biologist Lynn Margulis
developed endosymbiotic theory, which states that eukaryotes may have
been a product of one cell engulfing another, one living within another, and
evolving over time until the separate cells were no longer recognizable as
such. In 1967, Margulis introduced new work on the theory and
substantiated her findings through microbiological evidence. Although
Margulis’ work initially was met with resistance, this once-revolutionary
hypothesis is now widely accepted, with work progressing on uncovering
the steps involved in this evolutionary process and the key players involved.
Much still remains to be discovered about the origins of the cells that now
make up the cells in all living eukaryotes.
Broadly, it has become clear that many of our nuclear genes and the
molecular machinery responsible for replication and expression appear
closely related to those in Archaea. On the other hand, the metabolic
organelles and genes responsible for many energy-harvesting processes had
their origins in bacteria. Much remains to be clarified about how this
relationship occurred; this continues to be an exciting field of discovery in
biology. For instance, it is not known whether the endosymbiotic event that
led to mitochondria occurred before or after the host cell had a nucleus.
Such organisms would be among the extinct precursors of the last common
ancestor of eukaryotes.
Mitochondria
One of the major features distinguishing prokaryotes from eukaryotes is the
presence of mitochondria. Eukaryotic cells may contain anywhere from
one to several thousand mitochondria, depending on the cell’s level of
energy consumption. Each mitochondrion measures 1 to 10 or greater
micrometers in length and exists in the cell as an organelle that can be ovoid
to worm-shaped to intricately branched ({link]). Mitochondria arise from
the division of existing mitochondria; they may fuse together; and they may
be moved around inside the cell by interactions with the cytoskeleton.
However, mitochondria cannot survive outside the cell. As the atmosphere
was oxygenated by photosynthesis, and as successful aerobic prokaryotes
evolved, evidence suggests that an ancestral cell with some membrane
compartmentalization engulfed a free-living aerobic prokaryote, specifically
an alpha-proteobacterium, thereby giving the host cell the ability to use
oxygen to release energy stored in nutrients. Alpha-proteobacteria are a
large group of bacteria that includes species symbiotic with plants, disease
organisms that can infect humans via ticks, and many free-living species
that use light for energy. Several lines of evidence support that
mitochondria are derived from this endosymbiotic event. Most
mitochondria are shaped like alpha-proteobacteria and are surrounded by
two membranes, which would result when one membrane-bound organism
was engulfed into a vacuole by another membrane-bound organism. The
mitochondrial inner membrane is extensive and involves substantial
infoldings called cristae that resemble the textured, outer surface of alpha-
proteobacteria. The matrix and inner membrane are rich with the enzymes
necessary for aerobic respiration.
In this transmission electron
micrograph of mitochondria in a
mammalian lung cell, the
cristae, infoldings of the
mitochondrial inner membrane,
can be seen in cross-section.
(credit: Louise Howard)
Mitochondria divide independently by a process that resembles binary
fission in prokaryotes. Specifically, mitochondria are not formed from
scratch (de novo) by the eukaryotic cell; they reproduce within it and are
distributed with the cytoplasm when a cell divides or two cells fuse.
Therefore, although these organelles are highly integrated into the
eukaryotic cell, they still reproduce as if they are independent organisms
within the cell. However, their reproduction is synchronized with the
activity and division of the cell. Mitochondria have their own (usually)
circular DNA chromosome that is stabilized by attachments to the inner
membrane and carries genes similar to genes expressed by alpha-
proteobacteria. Mitochondria also have special ribosomes and transfer
RNAs that resemble these components in prokaryotes. These features all
support that mitochondria were once free-living prokaryotes.
Mitochondria that carry out aerobic respiration have their own genomes,
with genes similar to those in alpha-proteobacteria. However, many of the
genes for respiratory proteins are located in the nucleus. When these genes
are compared to those of other organisms, they appear to be of alpha-
proteobacterial origin. Additionally, in some eukaryotic groups, such genes
are found in the mitochondria, whereas in other groups, they are found in
the nucleus. This has been interpreted as evidence that genes have been
transferred from the endosymbiont chromosome to the host genome. This
loss of genes by the endosymbiont is probably one explanation why
mitochondria cannot live without a host.
Some living eukaryotes are anaerobic and cannot survive in the presence of
too much oxygen. Some appear to lack organelles that could be recognized
as mitochondria. In the 1970s to the early 1990s, many biologists suggested
that some of these eukaryotes were descended from ancestors whose
lineages had diverged from the lineage of mitochondrion-containing
eukaryotes before endosymbiosis occurred. However, later findings suggest
that reduced organelles are found in most, if not all, anaerobic eukaryotes,
and that all eukaryotes appear to carry some genes in their nuclei that are of
mitochondrial origin. In addition to the aerobic generation of ATP,
mitochondria have several other metabolic functions. One of these
functions is to generate clusters of iron and sulfur that are important
cofactors of many enzymes. Such functions are often associated with the
reduced mitochondrion-derived organelles of anaerobic eukaryotes.
Therefore, most biologists accept that the last common ancestor of
eukaryotes had mitochondria.
Plastids
Some groups of eukaryotes are photosynthetic. Their cells contain, in
addition to the standard eukaryotic organelles, another kind of organelle
called a plastid. When such cells are carrying out photosynthesis, their
plastids are rich in the pigment chlorophyll a and a range of other pigments,
called accessory pigments, which are involved in harvesting energy from
light. Photosynthetic plastids are called chloroplasts ([link]).
(a) (b)
(a) This chloroplast cross-section illustrates its elaborate
inner membrane organization. Stacks of thylakoid
membranes compartmentalize photosynthetic enzymes and
provide scaffolding for chloroplast DNA. (b) In this
micrograph of Elodea sp., the chloroplasts can be seen as
small green spheres. (credit b: modification of work by
Brandon Zierer; scale-bar data from Matt Russell)
Like mitochondria, plastids appear to have an endosymbiotic origin. This
hypothesis was also championed by Lynn Margulis. Plastids are derived
from cyanobacteria that lived inside the cells of an ancestral, aerobic,
heterotrophic eukaryote. This is called primary endosymbiosis, and plastids
of primary origin are surrounded by two membranes. The best evidence is
that this has happened twice in the history of eukaryotes. In one case, the
common ancestor of the major lineage/supergroup Archaeplastida took on a
cyanobacterial endosymbiont; in the other, the ancestor of the small
amoeboid rhizarian taxon, Paulinella, took on a different cyanobacterial
endosymbiont. Almost all photosynthetic eukaryotes are descended from
the first event, and only a couple of species are derived from the other.
Cyanobacteria are a group of Gram-negative bacteria with all the
conventional structures of the group. However, unlike most prokaryotes,
they have extensive, internal membrane-bound sacs called thylakoids.
Chlorophyll is a component of these membranes, as are many of the
proteins of the light reactions of photosynthesis. Cyanobacteria also have
the peptidoglycan wall and lipopolysaccharide layer associated with Gram-
negative bacteria.
Chloroplasts of primary origin have thylakoids, a circular DNA
chromosome, and ribosomes similar to those of cyanobacteria. Each
chloroplast is surrounded by two membranes. In the group of
Archaeplastida called the glaucophytes and in Paulinella, a thin
peptidoglycan layer is present between the outer and inner plastid
membranes. All other plastids lack this relictual cyanobacterial wall. The
outer membrane surrounding the plastid is thought to be derived from the
vacuole in the host, and the inner membrane is thought to be derived from
the plasma membrane of the symbiont.
There is also, as with the case of mitochondria, strong evidence that many
of the genes of the endosymbiont were transferred to the nucleus. Plastids,
like mitochondria, cannot live independently outside the host. In addition,
like mitochondria, plastids are derived from the division of other plastids
and never built from scratch. Researchers have suggested that the
endosymbiotic event that led to Archaeplastida occurred 1 to 1.5 billion
years ago, at least 5 hundred million years after the fossil record suggests
that eukaryotes were present.
Not all plastids in eukaryotes are derived directly from primary
endosymbiosis. Some of the major groups of algae became photosynthetic
by secondary endosymbiosis, that is, by taking in either green algae or red
algae (both from Archaeplastida) as endosymbionts ([link]ab). Numerous
microscopic and genetic studies have supported this conclusion. Secondary
plastids are surrounded by three or more membranes, and some secondary
plastids even have clear remnants of the nucleus of endosymbiotic alga.
Others have not “kept” any remnants. There are cases where tertiary or
higher-order endosymbiotic events are the best explanations for plastids in
some eukaryotes.
(b)
(a) Red algae and (b) green algae (visualized by light
microscopy) share similar DNA sequences with
photosynthetic cyanobacteria. Scientists speculate
that, in a process called endosymbiosis, an ancestral
prokaryote engulfed a photosynthetic cyanobacterium
that evolved into modern-day chloroplasts. (credit a:
modification of work by Ed Bierman; credit b:
modification of work by G. Fahnenstiel, NOAA;
scale-bar data from Matt Russell)
The ENDOSYMBIOTIC THEORY
@ Infoldings in the plasma In a second endosymbiotic
membrane of an ancestral event, the early eukaryote
prokaryote gave rise to consumed photosynthetic
endomembrane components, bacteria that evolved into
including a nucleus and chloroplasts.
endoplasmic reticulum.
Endoplasmic
Nucleus :
reticulum
e\
Modern photosynthetic
eukaryote
Photosynthetic
bacterium
Proto-eukaryote
In a first endosymbiotic event, Aerobic Mitochondrion
the ancestral eukaryote bacterium
consumed aerobic bacteria
that evolved into mitochondria.
Modern heterotrophic eukaryote
The first eukaryote may have originated from an ancestral
prokaryote that had undergone membrane proliferation,
compartmentalization of cellular function (into a nucleus,
lysosomes, and an endoplasmic reticulum), and the
establishment of endosymbiotic relationships with an
aerobic prokaryote, and, in some cases, a photosynthetic
prokaryote, to form mitochondria and chloroplasts,
respectively.
Note:
Evolution Connection
Secondary Endosymbiosis in Chlorarachniophytes
Endosymbiosis involves one cell engulfing another to produce, over time, a
coevolved relationship in which neither cell could survive alone. The
chloroplasts of red and green algae, for instance, are derived from the
engulfment of a photosynthetic cyanobacterium by an early prokaryote.
This leads to the question of the possibility of a cell containing an
endosymbiont to itself become engulfed, resulting in a secondary
endosymbiosis. Molecular and morphological evidence suggest that the
chlorarachniophyte protists are derived from a secondary endosymbiotic
event. Chlorarachniophytes are rare algae indigenous to tropical seas and
sand that can be classified into the rhizarian supergroup.
Chlorarachniophytes extend thin cytoplasmic strands, interconnecting
themselves with other chlorarachniophytes, in a cytoplasmic network.
These protists are thought to have originated when a eukaryote engulfed a
green alga, the latter of which had already established an endosymbiotic
relationship with a photosynthetic cyanobacterium ((link]).
ra Vestigial nucleus __Plastid
Primary Secondary
endossrblods endosymbiosis
One of the three
H hi membranes
eterotrophic surrounding the
eukaryote
plastid is lost.
The hypothesized process of endosymbiotic
events leading to the evolution of
chlorarachniophytes is shown. In a primary
endosymbiotic event, a heterotrophic
eukaryote consumed a cyanobacterium. In a
secondary endosymbiotic event, the cell
resulting from primary endosymbiosis was
consumed by a second cell. The resulting
organelle became a plastid in modern
chlorarachniophytes.
Several lines of evidence support that chlorarachniophytes evolved from
secondary endosymbiosis. The chloroplasts contained within the green
algal endosymbionts still are capable of photosynthesis, making
chlorarachniophytes photosynthetic. The green algal endosymbiont also
exhibits a stunted vestigial nucleus. In fact, it appears that
chlorarachniophytes are the products of an evolutionarily recent secondary
endosymbiotic event. The plastids of chlorarachniophytes are surrounded
by four membranes: The first two correspond to the inner and outer
membranes of the photosynthetic cyanobacterium, the third corresponds to
the green alga, and the fourth corresponds to the vacuole that surrounded
the green alga when it was engulfed by the chlorarachniophyte ancestor. In
other lineages that involved secondary endosymbiosis, only three
membranes can be identified around plastids. This is currently rectified as
a sequential loss of a membrane during the course of evolution.
The process of secondary endosymbiosis is not unique to
chlorarachniophytes. In fact, secondary endosymbiosis of green algae also
led to euglenid protists, whereas secondary endosymbiosis of red algae led
to the evolution of dinoflagellates, apicomplexans, and stramenopiles.
Atoms, Isotopes, Ions, and Molecules: The Building Blocks
""Through the discovery of Buchner, Biology was relieved of another
fragment of mysticism. The splitting up of sugar into CO> and alcohol is no
more the effect of a 'vital principle’ than the splitting up of cane sugar by
invertase. The history of this problem is instructive, as it warns us against
considering problems as beyond our reach because they have not yet found
their solution."" Jacques Loeb, in The Dynamics of Living Matter, (1906)
Loeb is referring to the Nobel Prize-winning experiments of Eduard
Buchner, who proved that cells are not necessary for cellular chemical
reactions to take place. This was one of the crucial steps toward the
synthesis of biology and chemistry that culminates in the modern-day
discipline we call biochemistry. The properties of matter are important in
the study of biochemistry (and biology), so we need to introduce some
chemical concepts to help us with that understanding. At its most
fundamental level, life is made up of matter. Matter is any substance that
occupies space and has mass. Elements are unique forms of matter with
specific chemical and physical properties that cannot be broken down into
smaller substances by ordinary chemical reactions. There are 118 elements,
but only 92 occur naturally. The remaining elements have only been
synthesized in laboratories, and are unstable.
Each element is designated by its chemical symbol, which is a single
capital letter or, when the first letter is already “taken” by another element,
a combination of two letters. Some elements follow the English term for the
element, such as C for carbon and Ca for calcium. Other elements’
chemical symbols derive from their Latin names; for example, the symbol
for sodium is Na, referring to natrium, the Latin word for sodium.
The four most abundant elements in all living organisms are oxygen (O),
carbon (C), hydrogen (H), and nitrogen (N). In the non-living world,
elements are found in different proportions, and some elements common to
living organisms are relatively rare on the earth as a whole, as shown in
[link]. For example, the atmosphere is rich in nitrogen and oxygen but
contains little carbon and hydrogen, while the earth’s crust, although it
contains oxygen and a small amount of hydrogen, has little nitrogen and
carbon. In spite of their differences in abundance, all elements and the
chemical reactions between them obey the same chemical and physical laws
regardless of whether they are a part of the living or non-living world.
Approximate Percentage of Elements in Living Organisms
(Humans) Compared to the Non-living World
Organisms Earth’s
Element (Humans) Atmosphere Crust
oo 65% 21% 46%
Carbon (C) 18% trace trace
Hydrogen ” “
(H) 10% trace 0.1%
Nitrogen ji )
(N) 3% 78% trace
The Structure of the Atom
To understand how elements come together, we must first discuss the
smallest component or building block of an element, the atom. An atom is
the smallest unit of matter that retains all of the chemical properties of an
element. For example, one gold atom has all of the properties of gold in that
it is a solid metal at room temperature. A gold coin is simply a very large
number of gold atoms molded into the shape of a coin and containing small
amounts of other elements known as impurities. Gold atoms cannot be
broken down into anything smaller while still retaining the properties of
gold.
An atom is composed of two regions: the nucleus, which is in the center of
the atom and contains protons and neutrons, and the outermost region of
the atom which holds its electrons in orbit around the nucleus, as illustrated
in [link]. Atoms contain protons, electrons, and neutrons. The only
exception is hydrogen (H), which is made of one proton and one electron,
with no neutrons.
Electrons
Elements, such as helium,
depicted here, are made up of
atoms. Atoms are made up of
protons and neutrons located
within the nucleus, with electrons
in orbitals surrounding the
nucleus.
Protons and neutrons have approximately the same mass, about 1.67 x 1074
grams. Scientists arbitrarily define this amount of mass as one atomic mass
unit (amu) or one Dalton, as shown in [link]. Although similar in mass,
protons and neutrons differ in their electric charge. A proton is positively
charged whereas a neutron is uncharged. Therefore, the number of
neutrons in an atom contributes significantly to its mass, but not to its
charge. Electrons are much smaller in mass than protons, weighing only
9.11 x 10°°8 grams, or about 1/1800 of an atomic mass unit. Hence, they do
not contribute much to an element’s overall atomic mass. Therefore, when
considering atomic mass, it is customary to ignore the mass of any electrons
and calculate the atom’s mass based on the number of protons and neutrons
alone. Although not significant contributors to mass, electrons do contribute
greatly to the atom’s charge, as each electron has a negative charge equal to
the positive charge of a proton. In uncharged, neutral atoms, the number of
electrons orbiting the nucleus is equal to the number of protons inside the
nucleus. In these atoms, the positive and negative charges cancel each other
out, leading to an atom with no net charge.
Accounting for the sizes of protons, neutrons, and electrons, most of the
volume of an atom—greater than 99 percent—is, in fact, empty space. With
all this empty space, one might ask why so-called solid objects do not just
pass through one another. The reason they do not is that the electrons that
surround all atoms are negatively charged and negative charges repel each
other.
Protons, Neutrons, and Electrons
Charge Mass (amu) Location
Proton +] i. nucleus
Neutron 0 1 nucleus
Electron —1 0 orbitals
Atomic Number and Mass
Atoms of each element contain a characteristic number of protons and
electrons. The number of protons determines an element’s atomic number
and is used to distinguish one element from another. Thus, an atom with
only one proton and one electron is always going to be an atom of
hydrogen; an atom with two electrons and two protons is an atom of
helium, etc. Unlike the fixed number of electrons and protons in atoms of
any particular element, however, the number of neutrons is variable. An
atom of hydrogen can have zero, one or two neutrons. Different numbers of
neutrons will not change the charge, but will change the mass of an atom.
These different forms, varying only in the number of neutrons, are called
isotopes. Together, the number of protons and the number of neutrons
determine an element’s mass number, as illustrated in [link]. Note that the
small contribution of mass from electrons is disregarded in calculating the
mass number. This approximation of mass can be used to easily calculate
how many neutrons an element has by simply subtracting the number of
protons from the mass number. Since an element’s isotopes will have
different mass numbers, scientists also determine the relative atomic mass
or standard atomic weight, which is the calculated mean of the mass
numbers for its naturally occurring isotopes. Often, the resulting number
contains a fraction. For example, the relative atomic mass of chlorine (Cl) is
35.45 because chlorine is composed of several isotopes, some (the majority)
with an atomic mass of 35 (17 protons and 18 neutrons) and some with an
atomic mass of 37 (17 protons and 20 neutrons).
Atomic number
Mass number
Carbon has an atomic number
of six, and two stable isotopes
with mass numbers of twelve
and thirteen, respectively. Its
relative atomic mass is 12.011.
Isotopes
Isotopes are different forms of an element that have the same number of
protons but a different number of neutrons. Some elements—such as
carbon, potassium, and uranium—have naturally occurring isotopes.
Carbon-12 contains six protons, six neutrons, and six electrons; therefore, it
has a mass number of 12 (six protons and six neutrons). Carbon-14 contains
six protons, eight neutrons, and six electrons; its atomic mass is 14 (six
protons and eight neutrons). These two alternate forms of carbon are
isotopes. Many isotopes are stable, but others are unstable, and can lose
neutrons, protons, and electrons, in order to attain a more stable atomic
configuration (lower level of potential energy). These unstable isotopes are
the radioactive isotopes, or radioisotopes. Radioactive decay (carbon-14
losing neutrons to eventually become carbon-12) describes the energy loss
that occurs when an unstable atom’s nucleus releases particles and
radiation.
Note:
Evolution Connection
Carbon Dating
Carbon is normally present in the atmosphere in the form of gaseous
compounds like carbon dioxide and methane. Carbon-14 ('4C) is a
naturally occurring radioisotope that is created in the atmosphere from
atmospheric !4N (nitrogen) by the addition of a neutron and the loss of a
proton because of cosmic rays. This is a continuous process, so more !4C is
always being created. As a living organism incorporates !4C initially as
carbon dioxide fixed in the process of photosynthesis, the relative amount
of /4C in its body is equal to the concentration of !4C in the atmosphere.
When an organism dies, it is no longer ingesting '4C, so the ratio between
'4C and !*C will decline as 4C decays gradually to '4N by a process called
beta decay—the emission of electrons or positrons. This decay gives off
energy in a slow process.
After approximately 5,730 years, half of the starting concentration of 4C
will have been converted back to ‘“N. The time it takes for half of the
original concentration of an isotope to decay back to its more stable form is
called its half-life. Because the half-life of !4C is long, it is used to date
formerly living objects such as old bones or wood. Comparing the ratio of
the '4C concentration found in an object to the amount of '4C detected in
the atmosphere, the amount of the isotope that has not yet decayed can be
determined. On the basis of this amount, the age of the material, such as
the pygmy mammoth shown in [link], can be calculated with accuracy if it
is not much older than about 50,000 years. Other elements have isotopes
with different half lives. For example, *°K (potassium-40) has a half-life of
1.25 billion years, and *?°U (Uranium 235) has a half-life of about 700
million years. Through the use of radiometric dating, scientists can study
the age of fossils or other remains of extinct organisms to understand how
organisms have evolved from earlier species.
The age of carbon-containing
remains less than about 50,000
years old, such as this pygmy
mammoth, can be determined
using carbon dating. (credit: Bill
Faulkner, NPS)
The Periodic Table
The different elements are organized and displayed in the periodic table.
Devised by Russian chemist Dmitri Mendeleev (1834—1907) in 1869, the
table groups elements that, although unique, share certain chemical
properties with other elements. The properties of elements are responsible
for their physical state at room temperature: they may be gases, solids, or
liquids. Elements also have specific chemical reactivity, the ability to
combine and to chemically bond with each other.
In the periodic table, shown in [link], the elements are organized and
displayed according to their atomic number and are arranged in a series of
rows and columns based on shared chemical and physical properties. In
addition to providing the atomic number for each element, the periodic
table also displays the element’s atomic mass. Looking at carbon, for
example, its symbol (C) and name appear, as well as its atomic number of
six (in the upper left-hand corner) and its relative atomic mass of 12.011.
Periodic Table of the Elements
[
fiona [_ ] Other non-metals |_| Noble gases
Number ; j
Symbol [_] Alkali metals {)] Lanthanides
1.01 Relative {| Transition metals [D) Actinides
Name Hydrogen Atomic Mass [_] Other metals [_] Unknown
chemical
properties
[[] Alkaline earth metals
|__| Halogens
The periodic table shows the atomic mass and atomic number of
each element. The atomic number appears above the symbol for
the element and the approximate atomic mass appears below it.
The periodic table groups elements according to chemical properties. The
differences in chemical reactivity between the elements are based on the
number and spatial distribution of an atom’s electrons. Atoms that
chemically react and bond to each other form molecules. Molecules are
simply two or more atoms chemically bonded together. Logically, when two
atoms chemically bond to form a molecule, their electrons, which form the
outermost region of each atom, come together first as the atoms form a
chemical bond.
Electron Shells and the Bohr Model
It should be stressed that there is a connection between the number of
protons in an element, the atomic number that distinguishes one element
from another, and the number of electrons it has. In all electrically neutral
atoms, the number of electrons is the same as the number of protons. Thus,
each element, at least when electrically neutral, has a characteristic number
of electrons equal to its atomic number.
An early model of the atom was developed in 1913 by Danish scientist
Niels Bohr (1885-1962). The Bohr model shows the atom as a central
nucleus containing protons and neutrons, with the electrons in circular
orbitals at specific distances from the nucleus, as illustrated in [link]. These
orbits form electron shells or energy levels, which are a way of visualizing
the number of electrons in the outermost shells. These energy levels are
designated by a number and the symbol “n.” For example, 1n represents the
first energy level located closest to the nucleus.
The Bohr model was
developed by Niels Bohrs in
1913. In this model, electrons
exist within principal shells.
An electron normally exists
in the lowest energy shell
available, which is the one
closest to the nucleus. Energy
from a photon of light can
bump it up to a higher energy
Shell, but this situation is
unstable, and the electron
quickly decays back to the
ground state. In the process, a
photon of light is released.
Electrons fill orbitals in a consistent order: they first fill the orbitals closest
to the nucleus, then they continue to fill orbitals of increasing energy further
from the nucleus. If there are multiple orbitals of equal energy, they will be
filled with one electron in each energy level before a second electron is
added. The electrons of the outermost energy level determine the energetic
stability of the atom and its tendency to form chemical bonds with other
atoms to form molecules.
Under standard conditions, atoms fill the inner shells first, often resulting in
a variable number of electrons in the outermost shell. The innermost shell
has a maximum of two electrons but the next two electron shells can each
have a maximum of eight electrons. This is known as the octet rule, which
States, with the exception of the innermost shell, that atoms are more stable
energetically when they have eight electrons in their valence shell, the
outermost electron shell. Examples of some neutral atoms and their electron
configurations are shown in [link]. Notice that in this [link], helium has a
complete outer electron shell, with two electrons filling its first and only
shell. Similarly, neon has a complete outer 2n shell containing eight
electrons. In contrast, chlorine and sodium have seven and one in their outer
shells, respectively, but theoretically they would be more energetically
stable if they followed the octet rule and had eight.
Bohr diagrams indicate how many electrons fill each
principal shell. Group 18 elements (helium, neon, and
argon are shown) have a full outer, or valence, shell. A
full valence shell is the most stable electron
configuration. Elements in other groups have partially
filled valence shells and gain or lose electrons to
achieve a stable electron configuration.
Understanding that the organization of the periodic table is based on the
total number of protons (and electrons) helps us know how electrons are
distributed among the outer shell. The periodic table is arranged in columns
and rows based on the number of electrons and where these electrons are
located. Take a closer look at the some of the elements in the table’s far
right column in [link]. The group 18 atoms helium (He), neon (Ne), and
argon (Ar) all have filled outer electron shells, making it unnecessary for
them to share electrons with other atoms to attain stability; they are highly
stable as single atoms. Their non-reactivity has resulted in their being
named the inert gases (or noble gases). Compare this to the group 1
elements in the left-hand column. These elements, including hydrogen (H),
lithium (Li), and sodium (Na), all have one electron in their outermost
shells. That means that they can achieve a stable configuration and a filled
outer shell by donating or sharing one electron with another atom or a
molecule such as water. Hydrogen will donate or share its electron to
achieve this configuration, while lithium and sodium will donate their
electron to become stable. As a result of losing a negatively charged
electron, they become positively charged ions. Group 17 elements,
including fluorine and chlorine, have seven electrons in their outmost
shells, so they tend to fill this shell with an electron from other atoms or
molecules, making them negatively charged ions. Group 14 elements, of
which carbon is the most important to living systems, have four electrons in
their outer shell allowing them to make several covalent bonds (discussed
below) with other atoms. Thus, the columns of the periodic table represent
the potential shared state of these elements’ outer electron shells that is
responsible for their similar chemical characteristics.
Chemical Reactions and Molecules
All elements are most stable when their outermost shell is filled with
electrons according to the octet rule. This is because it is energetically
favorable for atoms to be in that configuration and it makes them stable.
However, since not all elements have enough electrons to fill their
outermost shells, atoms form chemical bonds with other atoms thereby
obtaining the electrons they need to attain a stable electron configuration.
When two or more atoms chemically bond with each other, the resultant
chemical structure is a molecule. The familiar water molecule, H>O,
consists of two hydrogen atoms and one oxygen atom; these bond together
to form water, as illustrated in [link]. Atoms can form molecules by
donating, accepting, or sharing electrons to fill their outer shells.
Two or more atoms may bond with each other to form
a molecule. When two hydrogens and an oxygen share
electrons via covalent bonds, a water molecule is
formed.
Chemical reactions occur when two or more atoms bond together to form
molecules or when bonded atoms are broken apart. The substances used in
the beginning of a chemical reaction are called the reactants (usually found
on the left side of a chemical equation), and the substances found at the end
of the reaction are known as the products (usually found on the right side
of a chemical equation). An arrow is typically drawn between the reactants
and products to indicate the direction of the chemical reaction; this direction
is not always a “one-way street.” For the creation of the water molecule
shown above, the chemical equation would be:
Equation:
An example of a simple chemical reaction is the breaking down of
hydrogen peroxide molecules, each of which consists of two hydrogen
atoms bonded to two oxygen atoms (H 70>). The reactant hydrogen
peroxide is broken down into water, containing one oxygen atom bound to
two hydrogen atoms (HO), and oxygen, which consists of two bonded
oxygen atoms (O>). In the equation below, the reaction includes two
hydrogen peroxide molecules and two water molecules. This is an example
of a balanced chemical equation, wherein the number of atoms of each
element is the same on each side of the equation. According to the law of
conservation of matter, the number of atoms before and after a chemical
reaction should be equal, such that no atoms are, under normal
circumstances, created or destroyed.
Equation:
2H2O2 (hydrogen peroxide) —> 2H2O (water) + O, (oxygen)
Even though all of the reactants and products of this reaction are molecules
(each atom remains bonded to at least one other atom), in this reaction only
hydrogen peroxide and water are representative of a subclass of molecules
known as compounds: they contain atoms of more than one type of
element. Molecular oxygen, on the other hand, as shown in [link], consists
of two doubly bonded oxygen atoms and is not classified as a compound
but as an element.
The oxygen atoms in an O>) molecule are
joined by a double bond.
Some chemical reactions, such as the one shown above, can proceed in one
direction until the reactants are all used up. The equations that describe
these reactions contain a unidirectional arrow and are irreversible.
Reversible reactions are those that can go in either direction. In reversible
reactions, reactants are turned into products, but when the concentration of
product goes beyond a certain threshold (characteristic of the particular
reaction), some of these products will be converted back into reactants; at
this point, the designations of products and reactants are reversed. This back
and forth continues until a certain relative balance between reactants and
products occurs—a state called equilibrium. These situations of reversible
reactions are often denoted by a chemical equation with a double headed
arrow pointing towards both the reactants and products.
For example, in human blood, excess hydrogen ions (H") bind to
bicarbonate ions (HCO3°) forming an equilibrium state with carbonic acid
(H»CO3). If carbonic acid were added to this system, some of it would be
converted to bicarbonate and hydrogen ions.
Equation:
HCO; + Ht © HCO;
In biological reactions, however, equilibrium is rarely obtained because the
concentrations of the reactants or products or both are constantly changing,
often with a product of one reaction being a reactant for another. To return
to the example of excess hydrogen ions in the blood, the formation of
carbonic acid will be the major direction of the reaction. However, the
carbonic acid can also leave the body as carbon dioxide gas (via exhalation)
instead of being converted back to bicarbonate ion, thus driving the reaction
to the right by the chemical law known as law of mass action. These
reactions are important for maintaining the homeostasis of our blood.
Equation:
HCO; + Ht © H»CO3 © CQO, + H2O
Ions and Ionic Bonds
Some atoms are more stable when they gain or lose an electron (or possibly
two) and form ions. This fills their outermost electron shell and makes them
energetically more stable. Because the number of electrons does not equal
the number of protons, each ion has a net charge. Cations are positive ions
that are formed by losing electrons. Negative ions are formed by gaining
electrons and are called anions. Anions are designated by their elemental
name being altered to end in “-ide”: the anion of chlorine is called chloride,
and the anion of sulfur is called sulfide, for example.
This movement of electrons from one element to another is referred to as
electron transfer. As [link] illustrates, sodium (Na) only has one electron in
its outer electron shell. It takes less energy for sodium to donate that one
electron than it does to accept seven more electrons to fill the outer shell. If
sodium loses an electron, it now has 11 protons, 11 neutrons, and only 10
electrons, leaving it with an overall charge of +1. It is now referred to as a
sodium ion. Chlorine (Cl) in its lowest energy state (called the ground state)
has seven electrons in its outer shell. Again, it is more energy-efficient for
chlorine to gain one electron than to lose seven. Therefore, it tends to gain
an electron to create an ion with 17 protons, 17 neutrons, and 18 electrons,
giving it a net negative (—1) charge. It is now referred to as a chloride ion.
In this example, sodium will donate its one electron to empty its shell, and
chlorine will accept that electron to fill its shell. Both ions now satisfy the
octet rule and have complete outermost shells. Because the number of
electrons is no longer equal to the number of protons, each is now an ion
and has a +1 (sodium cation) or —1 (chloride anion) charge. Note that these
transactions can normally only take place simultaneously: in order for a
sodium atom to lose an electron, it must be in the presence of a suitable
recipient like a chlorine atom.
In the formation of an ionic compound,
metals lose electrons and nonmetals gain
electrons to achieve an octet.
Ionic bonds are formed between ions with opposite charges. For instance,
positively charged sodium ions and negatively charged chloride ions bond
together to make crystals of sodium chloride, or table salt, creating a
crystalline molecule with zero net charge.
Certain salts are referred to in physiology as electrolytes (including sodium,
potassium, and calcium), ions necessary for nerve impulse conduction,
muscle contractions and water balance. Many sports drinks and dietary
supplements provide these ions to replace those lost from the body via
sweating during exercise.
Covalent Bonds and Other Bonds and Interactions
Another way the octet rule can be satisfied is by the sharing of electrons
between atoms to form covalent bonds. Covalent bonds are much more
common than ionic bonds in the molecules of living organisms, and often
the covalent bonds discussed in these systems are stronger than the ionic
bonds. So, Biologists often think of covalent bonds as being stronger than
ionic bonds, in fact, ionic bonds can produce some of the strongest bonds
on the planet i.e. steel. Since covalent bonds are commonly found in
carbon-based organic molecules, such as carbohydrates, our DNA and
proteins are the bonds we discuss most, and covalent bonds are also found
in inorganic molecules like H»O, CO», and Op», Biologists often think of
covalent bonds begin the strongest. In addition, One, two, or three pairs of
electrons may be shared, making single, double, and triple bonds,
respectively. The more covalent bonds between two atoms, the stronger
their connection. Thus, triple bonds are the strongest in biologic systems.
The strength of different levels of covalent bonding is one of the main
reasons living organisms have a difficult time in acquiring nitrogen for use
in constructing their molecules, even though molecular nitrogen, No, is the
most abundant gas in the atmosphere. Molecular nitrogen consists of two
nitrogen atoms triple bonded to each other and, as with all molecules, the
sharing of these three pairs of electrons between the two nitrogen atoms
allows for the filling of their outer electron shells, making the molecule
more stable than the individual nitrogen atoms. This strong triple bond
makes it difficult for living systems to break apart this nitrogen in order to
use it as constituents of proteins and DNA.
The formation of water molecules provides an example of covalent
bonding. The hydrogen and oxygen atoms that combine to form water
molecules are bound together by covalent bonds, as shown in [link]. The
electron from the hydrogen splits its time between the incomplete outer
shell of the hydrogen atoms and the incomplete outer shell of the oxygen
atoms. To completely fill the outer shell of oxygen, which has six electrons
in its outer shell but which would be more stable with eight, two electrons
(one from each hydrogen atom) are needed: hence the well-known formula
H,O. The electrons are shared between the two elements to fill the outer
shell of each, making both elements more stable.
Polar Covalent Bonds
There are two types of covalent bonds: polar and nonpolar. In a polar
covalent bond, shown in [link], the electrons are unequally shared by the
atoms and are attracted more to one nucleus than the other. Because of the
unequal distribution of electrons between the atoms of different elements, a
slightly positive (6+) or slightly negative (6—) charge develops. This partial
charge is an important property of water and accounts for many of its
characteristics.
Water is a polar molecule, with the hydrogen atoms acquiring a partial
positive charge and the oxygen a partial negative charge. This occurs
because the nucleus of the oxygen atom is more attractive to the electrons
of the hydrogen atoms than the hydrogen nucleus is to the oxygen’s
electrons. Thus oxygen has a higher electronegativity than hydrogen and
the shared electrons spend more time in the vicinity of the oxygen nucleus
than they do near the nucleus of the hydrogen atoms, giving the atoms of
oxygen and hydrogen slightly negative and positive charges, respectively.
Another way of stating this is that the probability of finding a shared
electron near an oxygen nucleus is more likely than finding it near a
hydrogen nucleus. Either way, the atom’s relative electronegativity
contributes to the development of partial charges whenever one element is
significantly more electronegative than the other, and the charges generated
by these polar bonds may then be used for the formation of hydrogen bonds
based on the attraction of opposite partial charges. (Hydrogen bonds, which
are discussed in detail below, are weak bonds between slightly positively
charged hydrogen atoms to slightly negatively charged atoms in other
molecules.) Since macromolecules often have atoms within them that differ
in electronegativity, polar bonds are often present in organic molecules.
Nonpolar Covalent Bonds
Nonpolar covalent bonds form between two atoms of the same element or
between different elements that share electrons equally. For example,
molecular oxygen (O2) is nonpolar because the electrons will be equally
distributed between the two oxygen atoms.
Another example of a nonpolar covalent bond is methane (CH,), also
shown in [link]. Carbon has four electrons in its outermost shell and needs
four more to fill it. It gets these four from four hydrogen atoms, each atom
providing one, making a stable outer shell of eight electrons. Carbon and
hydrogen do not have the same electronegativity but are similar; thus,
nonpolar bonds form. The hydrogen atoms each need one electron for their
outermost shell, which is filled when it contains two electrons. These
elements share the electrons equally among the carbons and the hydrogen
atoms, creating a nonpolar covalent molecule.
Bond type Molecular shape Molecular type
+ 3+
Polar covalent
Carbon
dioxide
Polar covalent Linear
Whether a molecule is polar or nonpolar
depends both on bond type and molecular
shape. Both water and carbon dioxide have
polar covalent bonds, but carbon dioxide is
linear, so the partial charges on the molecule
cancel each other out.
Hydrogen Bonds and Van Der Waals Interactions
Ionic and covalent bonds between elements require energy to break. Ionic
bonds are not as strong as covalent, which determines their behavior in
biological systems. However, not all bonds are ionic or covalent bonds.
Weaker bonds can also form between molecules. Two weak bonds that
occur frequently are hydrogen bonds and van der Waals interactions.
Without these two types of bonds, life as we know it would not exist.
Hydrogen bonds provide many of the critical, life-sustaining properties of
water and also stabilize the structures of proteins and DNA, the building
block of cells.
When polar covalent bonds containing hydrogen form, the hydrogen in that
bond has a slightly positive charge because hydrogen’s electron is pulled
more strongly toward the other element and away from the hydrogen.
Because the hydrogen is slightly positive, it will be attracted to neighboring
negative charges. When this happens, a weak interaction occurs between the
6‘ of the hydrogen from one molecule and the é— charge on the more
electronegative atoms of another molecule, usually oxygen or nitrogen, or
within the same molecule. This interaction is called a hydrogen bond. This
type of bond is common and occurs regularly between water molecules.
Individual hydrogen bonds are weak and easily broken; however, they occur
in very large numbers in water and in organic polymers, creating a major
force in combination. Hydrogen bonds are also responsible for zipping
together the DNA double helix.
Like hydrogen bonds, van der Waals interactions are weak attractions or
interactions between molecules. Van der Waals attractions can occur
between any two or more molecules and are dependent on slight
fluctuations of the electron densities, which are not always symmetrical
around an atom. For these attractions to happen, the molecules need to be
very close to one another. These bonds, along with hydrogen bonds, help
form the three-dimensional structure of the proteins in our cells that is
necessary for their proper function.
Water: the Molecule of Life
Introduction
"Life can be thought of as water kept in the right temperature in the right
atmosphere in the right light for a long enough period of time." Norman J.
Berrill, You and the Universe, pg. 45, 1958
Why do scientists spend time looking for water on other planets? Why is
water so important? It is because water is essential to life as we know it.
Water is one of the more abundant molecules and the one most critical to
life on Earth. Approximately 70 percent of the human body is made up of
water. Without it, life as we know it simply would not exist.
The polarity of the water molecule and its resulting hydrogen bonding
make water a unique substance with special properties that are intimately
tied to the processes of life. Life originally evolved in a watery
environment, and most of an organism’s cellular chemistry and metabolism
occur inside the watery contents of the cell’s cytoplasm. Special properties
of water are its high heat capacity and heat of vaporization, its ability to
dissolve polar molecules, its cohesive and adhesive properties, and its
dissociation into ions that leads to the generation of pH. Understanding
these characteristics of water helps to elucidate its importance in
maintaining life.
Water’s Polarity
One of water’s important properties is that it is composed of polar
molecules: the hydrogen and oxygen within water molecules (H.O) form
polar covalent bonds. While there is no net charge to a water molecule, the
polarity of water creates a slightly positive charge on hydrogen and a
slightly negative charge on oxygen, contributing to water’s properties of
attraction. Water’s charges are generated because oxygen is more
electronegative than hydrogen, making it more likely that a shared electron
would be found near the oxygen nucleus than the hydrogen nucleus, thus
generating the partial negative charge near the oxygen.
As a result of water’s polarity, each water molecule attracts other water
molecules because of the opposite charges between water molecules,
forming hydrogen bonds. Water also attracts or is attracted to other polar
molecules and ions. A polar substance that interacts readily with or
dissolves in water is referred to as hydrophilic (hydro- = “water”; -philic =
“loving”). In contrast, non-polar molecules such as oils and fats do not
interact well with water, as shown in [link] and separate from it rather than
dissolve in it, as we see in salad dressings containing oil and vinegar (an
acidic water solution). These nonpolar compounds are called hydrophobic
(hydro- = “water”; -phobic = “fearing”).
Oil and water do not mix. As this
macro image of oil and water
shows, oil does not dissolve in
water but forms droplets instead.
This is due to it being a nonpolar
compound. (credit: Gautam
Dogra).
Water’s States: Gas, Liquid, and Solid
The formation of hydrogen bonds is an important quality of the liquid water
that is crucial to life as we know it. As water molecules make hydrogen
bonds with each other, water takes on some unique chemical characteristics
compared to other liquids and, since living things have a high water
content, understanding these chemical features is key to understanding life.
In liquid water, hydrogen bonds are constantly formed and broken as the
water molecules slide past each other. The breaking of these bonds is
caused by the motion (kinetic energy) of the water molecules due to the
heat contained in the system. When the heat is raised as water is boiled, the
higher kinetic energy of the water molecules causes the hydrogen bonds to
break completely and allows water molecules to escape into the air as gas
(steam or water vapor). On the other hand, when the temperature of water is
reduced and water freezes, the water molecules form a crystalline structure
maintained by hydrogen bonding (there is not enough energy to break the
hydrogen bonds) that makes ice less dense than liquid water, a phenomenon
not seen in the solidification of other liquids.
Water’s lower density in its solid form is due to the way hydrogen bonds are
oriented as it freezes: the water molecules are pushed farther apart
compared to liquid water. With most other liquids, solidification when the
temperature drops includes the lowering of kinetic energy between
molecules, allowing them to pack even more tightly than in liquid form and
giving the solid a greater density than the liquid.
The lower density of ice, illustrated and pictured in [link], an anomaly,
causes it to float at the surface of liquid water, such as in an iceberg or in
the ice cubes in a glass of ice water. In lakes and ponds, ice will form on the
surface of the water creating an insulating barrier that protects the animals
and plant life in the pond from freezing. Without this layer of insulating ice,
plants and animals living in the pond would freeze in the solid block of ice
and could not survive. The detrimental effect of freezing on living
organisms is caused by the expansion of ice relative to liquid water. The ice
crystals that form upon freezing rupture the delicate membranes essential
for the function of living cells, irreversibly damaging them. Cells can only
survive freezing if the water in them is temporarily replaced by another
liquid like glycerol.
Hydrogen bonding makes ice less dense than liquid
water. The (a) lattice structure of ice makes it less
dense than the freely flowing molecules of liquid
water, enabling it to (b) float on water. (credit a:
modification of work by Jane Whitney, image created
using Visual Molecular Dynamics (VMD)
software! !otmote!. credit b: courtesy David A. Rintoul)
W. Humphrey W., A. Dalke, and K. Schulten, “VMD
—Visual Molecular Dynamics,” Journal of Molecular
Graphics 14 (1996): 33-38.
Water’s High Heat Capacity
Water’s high heat capacity is a property caused by hydrogen bonding
among water molecules. Water has the highest specific heat capacity of any
liquids. Specific heat is defined as the amount of heat one gram of a
substance must absorb or lose to change its temperature by one degree
Celsius. For water, this amount is one calorie. It therefore takes water a long
time to heat and long time to cool. In fact, the specific heat capacity of
water is about five times more than that of sand. This explains why the land
cools faster than the sea. Due to its high heat capacity, water is used by
warm blooded animals to more evenly disperse heat in their bodies: it acts
in a similar manner to a car’s cooling system, transporting heat from warm
places to cool places, causing the body to maintain a more even
temperature.
Water’s Heat of Vaporization
Water also has a high heat of vaporization, the amount of energy required
to change one gram of a liquid substance to a gas. A considerable amount of
heat energy (586 cal) is required to accomplish this change in water. This
process occurs on the surface of water. As liquid water heats up, hydrogen
bonding makes it difficult to separate the liquid water molecules from each
other, which is required for it to enter its gaseous phase (steam). As a result,
water acts as a heat sink or heat reservoir and requires much more heat to
boil than does a liquid such as ethanol (grain alcohol), whose hydrogen
bonding with other ethanol molecules is weaker than water’s hydrogen
bonding. Eventually, as water reaches its boiling point of 100° Celsius
(212° Fahrenheit), the heat is able to break the hydrogen bonds between the
water molecules, and the kinetic energy (motion) between the water
molecules allows them to escape from the liquid as a gas. Even when below
its boiling point, water’s individual molecules acquire enough energy from
other water molecules such that some surface water molecules can escape
and vaporize: this process is known as evaporation.
The fact that hydrogen bonds need to be broken for water to evaporate
means that a substantial amount of energy is used in the process. As the
water evaporates, energy is taken up by the process, cooling the
environment where the evaporation is taking place. In many living
organisms, including in humans, the evaporation of sweat, which is 90
percent water, allows the organism to cool so that homeostasis of body
temperature can be maintained.
Water’s Solvent Properties
Since water is a polar molecule with slightly positive and slightly negative
charges, ions and polar molecules can readily dissolve in it. Therefore,
water is referred to as a solvent, a substance capable of dissolving other
polar molecules and ionic compounds. The charges associated with these
molecules will form hydrogen bonds with water, surrounding the particle
with water molecules. This is referred to as a sphere of hydration, or a
hydration shell, as illustrated in [link] and serves to keep the particles
separated or dispersed in the water.
When ionic compounds are added to water, the individual ions react with
the polar regions of the water molecules and their ionic bonds are disrupted
in the process of dissociation. Dissociation occurs when atoms or groups of
atoms break off from molecules and form ions. Consider table salt (NaCl, or
sodium chloride): when NaCl crystals are added to water, the molecules of
NaCl] dissociate into Na* and Cl ions, and spheres of hydration form
around the ions, illustrated in [link]. The positively charged sodium ion is
surrounded by the partially negative charge of the water molecule’s oxygen.
The negatively charged chloride ion is surrounded by the partially positive
charge of the hydrogen on the water molecule.
When table salt (NaCl) is
mixed in water, spheres of
hydration are formed around
the ions.
Water’s Cohesive and Adhesive Properties
Have you ever filled a glass of water to the very top and then slowly added
a few more drops? Before it overflows, the water forms a dome-like shape
above the rim of the glass. This water can stay above the glass because of
the property of cohesion. In cohesion, water molecules are attracted to each
other (because of hydrogen bonding), keeping the molecules together at the
liquid-gas (water-air) interface, although there is no more room in the glass.
Cohesion allows for the development of surface tension, the capacity of a
substance to withstand being ruptured when placed under tension or stress.
This is also why water forms droplets when placed on a dry surface rather
than being flattened out by gravity. When a small scrap of paper is placed
onto the droplet of water, the paper floats on top of the water droplet even
though paper is denser (heavier) than the water. Cohesion and surface
tension keep the hydrogen bonds of water molecules intact and support the
item floating on the top. It’s even possible to “float” a needle on top of a
glass of water if it is placed gently without breaking the surface tension, as
shown in [link].
The weight of the needle is pulling
the surface downward; at the same
time, the surface tension is pulling
it up, suspending it on the surface
of the water and keeping it from
sinking. Notice the indentation in
the water around the needle.
(credit: Cory Zanker)
These cohesive forces are related to water’s property of adhesion, or the
attraction between water molecules and other molecules. This attraction is
sometimes stronger than water’s cohesive forces, especially when the water
is exposed to charged surfaces such as those found on the inside of thin
glass tubes known as capillary tubes. Adhesion is observed when water
“climbs” up the tube placed in a glass of water: notice that the water
appears to be higher on the sides of the tube than in the middle. This is
because the water molecules are attracted to the charged glass walls of the
capillary more than they are to each other and therefore adhere to it. This
type of adhesion is called capillary action, and is illustrated in [link].
Capillary tube
_
Capillary
attraction
Capillary action in a glass tube is
caused by the adhesive forces
exerted by the internal surface of
the glass exceeding the cohesive
forces between the water
molecules themselves. (credit:
modification of work by Pearson-
Scott Foresman, donated to the
Wikimedia Foundation)
Why are cohesive and adhesive forces important for life? Cohesive and
adhesive forces are important for the transport of water from the roots to the
leaves in plants. These forces create a “pull” on the water column. This pull
results from the tendency of water molecules being evaporated on the
surface of the plant to stay connected to water molecules below them, and
so they are pulled along. Plants use this natural phenomenon to help
transport water from their roots to their leaves. Without these properties of
water, plants would be unable to receive the water and the dissolved
minerals they require. In another example, insects such as the water strider,
shown in [link], use the surface tension of water to stay afloat on the surface
layer of water and even mate there.
Water’s cohesive and adhesive
properties allow this water strider
(Gerris sp.) to stay afloat. (credit:
Tim Vickers)
pH, Acids, and Bases
The pH of a solution indicates its acidity or alkalinity.
Equation:
H,O(I) «+ Ht (aq) + OH (aq)
Litmus or pH paper, filter paper that has been treated with a natural water-
soluble dye so it can be used as a pH indicator, to test how much acid
(acidity) or base (alkalinity) exists in a solution. You might have even used
some to test whether the water in a swimming pool is properly treated. In
both cases, the pH test measures the concentration of hydrogen ions in a
given solution.
Hydrogen ions are spontaneously generated in pure water by the
dissociation (ionization) of a small percentage of water molecules into
equal numbers of hydrogen (H") ions and hydroxide (OH’) ions. While the
hydroxide ions are kept in solution by their hydrogen bonding with other
water molecules, the hydrogen ions, consisting of naked protons, are
immediately attracted to un-ionized water molecules, forming hydronium
ions (H30°). Still, by convention, scientists refer to hydrogen ions and their
concentration as if they were free in this state in liquid water.
The concentration of hydrogen ions dissociating from pure water is 1 x 1077
moles H* ions per liter of water. Moles (mol) are a way to express the
amount of a substance (which can be atoms, molecules, ions, etc), with one
mole being equal to 6.02 x 10*° particles of the substance. Therefore, 1
mole of water is equal to 6.02 x 107? water molecules. The pH is calculated
as the negative of the base 10 logarithm of this concentration (see below).
The logi9 of 1 x 10°” is -7.0, and the negative of this number (indicated by
the “p” of “pH”) yields a pH of 7.0, which is also known as neutral pH. The
pH inside of human cells and blood are examples of two areas of the body
where near-neutral pH is maintained.
pH = -log;)[Hydrogen Ion]
Non-neutral pH readings result from dissolving acids or bases in water.
Using the negative logarithm to generate positive integers, high
concentrations of hydrogen ions yield a low pH number, whereas low levels
of hydrogen ions result in a high pH. An acid is a substance that increases
the concentration of hydrogen ions (H‘) in a solution, usually by having one
of its hydrogen atoms dissociate. A base provides either hydroxide ions
(OH_) or other negatively charged ions that combine with hydrogen ions,
reducing their concentration in the solution and thereby raising the pH. In
cases where the base releases hydroxide ions, these ions bind to free
hydrogen ions, generating new water molecules.
The stronger the acid, the more readily it donates H*. For example,
hydrochloric acid (HCl) completely dissociates into hydrogen and chloride
ions and is highly acidic, whereas the acids in tomato juice or vinegar do
not completely dissociate and are considered weak acids. Conversely,
strong bases are those substances that readily donate OH or take up
hydrogen ions. Sodium hydroxide (NaOH) and many household cleaners
are highly alkaline and give up OH™ rapidly when placed in water, thereby
raising the pH. An example of a weak basic solution is seawater, which has
a pH near 8.0, close enough to neutral pH that marine organisms adapted to
this saline environment are able to thrive in it.
The pH scale is, as previously mentioned, an inverse logarithm and ranges
from 0 to 14 ([link]). Anything below 7.0 (ranging from 0.0 to 6.9) is
acidic, and anything above 7.0 (from 7.1 to 14.0) is alkaline. Extremes in
PH in either direction from 7.0 are usually considered inhospitable to life.
The pH inside cells (6.8) and the pH in the blood (7.4) are both very close
to neutral. However, the environment in the stomach is highly acidic, with a
PH of 1 to 2. So how do the cells of the stomach survive in such an acidic
environment? How do they homeostatically maintain the near neutral pH
inside them? The answer is that they cannot do it and are constantly dying.
New stomach cells are constantly produced to replace dead ones, which are
digested by the stomach acids. It is estimated that the lining of the human
stomach is completely replaced every seven to ten days.
13 Bleach
12 Soapy water
11 Ammonia solution
10 Milk of magnesia
9 Baking soda
8 Sea water
7 Distilled water
6 Urine
5 Black coffee
4 Tomato juice
3 Orange juice
2 Lemon juice
1 Gastric acid
0
The pH scale measures the
concentration of hydrogen
ions (H*) in a solution.
(credit: modification of work
by Edward Stevens)
Introduction to Biological Molecules
Introduction
"The most fundamental difference between compounds of low molecular
weight and macromolecular compounds resides in the fact that the latter
may exhibit properties that cannot be deduced from a close examination of
the low molecular weight materials. Not very different structures can be
obtained from a few building blocks, but if 10,000 or 100,000 bloocks are
at hand, the most varied structures become possible..." Hermann Staudinger,
quoted in R. Oesper, The Human Side of Scientists, pg. 75, 1975
Biological macromolecules are large molecules, necessary for life (Table
1), and these large molecules are made from smaller organic molecules. As
noted above, there is an almost infinite variety of possible structures for
macromolecules, since both the composition and the bonds lining the
components can vary tremendously. There are four major classes of
biological macromolecules (carbohydrates, lipids, proteins, and nucleic
acids). As we explore these molecules, think about how each class makes
up important cell components and perform a wide array of functions. Since
all these biological macromolecules contain carbon, we call them are
organic molecules. In addition, the ratio of carbon, hydrogen, oxygen,
nitrogen, and additional minor elements determines the class of biological
molecules.
Type of Function Location in Cell
Molecule
Carbohydrates
Simple Sugars Provide Quick Energy Cytoplasm
Complex Support Cells (cellulose, Cell Walls
Carbohydrates chitin); Store energy (cellulose,
(cellulose,
chitin, starch,
glycogen)
Lipids
Triglycerides
(fats and oils)
Phospholipids
Sterols and
Steroids
Waxes
Proteins
Nucleic Acids
(DNA and
RNA)
(starch, glycogen)
Store Energy
Major component of
biological membranes
Stabilize animal plasma
membranes; sex
hormones
Waterproofing
Movement, Immunity,
Energy Source,
Enzymes, Structural
Support,
Communication,
Hormones,
Store and use genetic
information
A summary of the Biological Molecules
chitin);
cytoplasm
(starch,
glycogen)
Cytoplasm
Plasma
membranes
animal plasma
membranes
Cell Walls
(plants),Excreted
(animals)
In all parts of the
cell
DNA (Nucleus)
RNA
(Cytoplasm, and
Rough
Endoplasmic
Reticulum
Chemical Reactions of Biological Macromolecules
Condensation Reaction
Most macromolecules are made from single subunits, or building blocks,
called monomers. The monomers combine with each other using covalent
bonds to form larger molecules known as polymers. In doing so, monomers
release water molecules as byproducts. This type of reaction is known as
condensation reaction.
CH20OH CH20H CH20H CH20H
fe) fe) OH H Oo
H - OH
+ —> + H20
HO OH HO OH HO O H
OH OH OH OH
In the condensation reaction depicted above, two molecules of
glucose are linked together to form the dissacharide maltose. In the
process, a water molecule is formed.
In a condensation reaction ({link]), the hydrogen of one monomer combines
with the hydroxyl group of another monomer, releasing a molecule of water.
At the same time, the monomers share electrons and form covalent bonds.
As additional monomers join, this chain of repeating monomers forms a
polymer. Different types of monomers can combine in many configurations,
giving rise to a diverse group of macromolecules. Even one kind of
monomer can combine in a variety of ways to form several different
polymers: for example, glucose monomers are the constituents of starch,
glycogen, and cellulose.
Hydrolysis
Polymers are broken down into monomers in a process known as
hydrolysis, which means “to split water,” a reaction in which a water
molecule is used during the breakdown ([link]). During these reactions, the
polymer is broken into two components: one part gains a hydrogen atom
(H+) and the other gains a hydroxyl molecule (OH—) from a split water
molecule.
CH,OH CH,OH CH,OH CH,OH
OH H O OH O
OH H
O
H H
HO O oy 1° OH
OH OH OH OH
In the hydrolysis reaction shown here, the disaccharide maltose is
broken down to form two glucose monomers. Note that this reaction
is the reverse of the condensation reaction shown in [link].
Condensation and hydrolysis reactions are catalyzed, or “sped up,” by
specific enzymes; condensation reactions involve the formation of new
bonds, requiring energy, while hydrolysis reactions break bonds and release
energy. These reactions are similar for most macromolecules, but each
monomer and polymer reaction is specific for its class. For example, in our
bodies, food is hydrolyzed, or broken down, into smaller molecules by
catalytic enzymes in the digestive system. This allows for easy absorption
of nutrients by cells in the intestine. Each macromolecule is broken down
by a specific enzyme. For instance, carbohydrates are broken down by
amylase, sucrase, lactase, or maltase. Proteins are broken down by the
enzymes pepsin and peptidase, and by hydrochloric acid. Lipids are broken
down by lipases. Breakdown of these macromolecules provides energy for
cellular activities.
Carbohydrates
Introduction
"T called it ignose, not knowing which carbohydrate it was. This name was
turned down by my editor. 'God-nose' was not more successful, so in the
end 'hexuronic acid' was agreed upon. To-day the substance is called
‘ascorbic acid' and I will use this name." Albert Szent-Gyorgyi, Studies on
Biological Oxidation and Some of its Catalysts (C4 Dicarboxylic Acids,
Vitamin C and P Etc.), pg. 73, 1937
Most people(except perhaps Szent-Gyorgyi's editor) are familiar with
carbohydrates, one type of macromolecule, especially when it comes to
what we eat. To lose weight, some individuals adhere to “low-carb” diets.
Athletes, in contrast, often “carb-load” before important competitions to
ensure that they have enough energy to compete at a high level.
Carbohydrates are, in fact, an essential part of our diet; grains, fruits, and
vegetables are all natural sources of carbohydrates. Carbohydrates provide
energy to the body, particularly through glucose, a simple sugar that is a
component of starch and an ingredient in many staple foods. Carbohydrates
also have other important functions in humans, animals, and plants. And, as
you can infer from the epigraph above, the suffix "-ose" is a good clue that
a word describes a carboydrate of some sort.
Molecular Structures
Carbohydrates can be represented by the stoichiometric formula (CH)0),,
where n is the number of carbons in the molecule. In other words, the ratio
of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. This
formula also explains the origin of the term “carbohydrate”: the
components are carbon (“carbo”) and the components of water (hence,
“hydrate’”). Carbohydrates are classified into three subtypes:
monosaccharides, disaccharides, and polysaccharides.
Monosaccharides
Monosaccharides (mono- = “one”; sacchar- = “sweet”) are simple sugars,
the most common of which is glucose. In monosaccharides, the number of
carbons usually ranges from three to seven. Most monosaccharide names
end with the suffix -ose. Depending on the number of carbons in the sugar,
they also may be known as trioses (three carbons), pentoses (five carbons),
and or hexoses (six carbons). See [link] for an illustration of the
monosaccharides.
MONOSACCHARIDES
Glyceraldehyde Dihydroxyacetone
Ribose
Monosaccharides are classified based on the
position of their carbonyl group and the
number of carbons in the backbone. Aldoses
have a carbonyl group (indicated in green) at
the end of the carbon chain, and ketoses
have a carbonyl group in the middle of the
carbon chain. Trioses, pentoses, and hexoses
have three, five, and six carbon backbones,
respectively.
The chemical formula for glucose is CgH; 0g. In humans, glucose is an
important source of energy. During cellular respiration, energy is released
from glucose, and that energy is used to help make adenosine triphosphate
(ATP). Plants synthesize glucose using carbon dioxide and water, and
glucose in turn is used for energy requirements for the plant. Excess glucose
is often stored as starch that is catabolized (the breakdown of larger
molecules by cells) by humans and other animals that feed on plants.
Galactose (part of lactose, or milk sugar) and fructose (found in sucrose, in
fruit) are other common monosaccharides. Although glucose, galactose, and
fructose all have the same chemical formula (CgH, Og), they differ
structurally and chemically (and are known as isomers) because of the
different arrangement of functional groups around the asymmetric carbon;
all of these monosaccharides have more than one asymmetric carbon
(Llink]).
Glucose Galactose Fructose
Glucose, galactose, and fructose are all
hexoses. They are structural isomers,
meaning they have the same chemical
formula (CgH; O¢) but a different
arrangement of atoms.
Monosaccharides can exist as a linear chain or as ring-shaped molecules; in
aqueous solutions they are usually found in ring forms ({link]). Glucose in a
ring form can have two different arrangements of the hydroxyl group (OH)
around the anomeric carbon (carbon 1 that becomes asymmetric in the
process of ring formation). If the hydroxyl group is below carbon number 1
in the sugar, it is said to be in the alpha (a) position, and if it is above the
plane, it is said to be in the beta () position.
Conversion between Linear and Ring Forms of Glucose
Glucose
CH,OH
a Glucose
CH,OH
Fructose
Five and six carbon monosaccharides exist
in equilibrium between linear and ring
forms. When the ring forms, the side chain it
closes on is locked into an a or f position.
Fructose and ribose also form rings,
although they form five-membered rings as
opposed to the six-membered ring of
glucose.
Disaccharides
Disaccharides (di- = “two”) form when two monosaccharides undergo a
condensation reaction (also known as a dehydration synthesis). During this
process, the hydroxyl group of one monosaccharide combines with the
hydrogen of another monosaccharide, releasing a molecule of water and
forming a covalent bond. A covalent bond formed between a carbohydrate
molecule and another molecule (in this case, between two
monosaccharides) is known as a glycosidic bond ([link]). Glycosidic bonds
(also called glycosidic linkages) can be of the alpha or the beta type.
H OH
Glucose
CH,OH
H OH f
Sucrose Glycosidic Bond
Sucrose is formed when a monomer of
glucose and a monomer of fructose are
joined in a condensation reaction to form a
glycosidic bond. In the process, a water
molecule is lost. By convention, the carbon
atoms in a monosaccharide are numbered
from the terminal carbon closest to the
carbonyl] group. In sucrose, a glycosidic
linkage is formed between carbon 1 in
glucose and carbon 2 in fructose.
Common disaccharides include lactose, maltose, and sucrose ((link]).
Lactose is a disaccharide consisting of the monomers glucose and galactose.
It is found naturally in milk. Maltose, or malt sugar, is a disaccharide
formed by a condensation reaction between two glucose molecules. The
most common disaccharide is sucrose, or table sugar, which is composed of
the monomers glucose and fructose.
CH,OH CH,OH
Maltose
CH,OH
1)
OH
CH,OH
OH
[@)
OH Oo
OH
OH
Lactose OH
CH,OH
CH,OH
Oo OH
H HO
CH,OH
H OH OH H
Sucrose
Common disaccharides include maltose
(grain sugar), lactose (milk sugar), and
sucrose (table sugar).
Polysaccharides
A long chain of monosaccharides linked by glycosidic bonds is known as a
polysaccharide (poly- = “many”). The chain may be branched or
unbranched, and it may contain different types of monosaccharides. The
molecular weight may be 100,000 daltons or more depending on the
number of monomers joined. Starch, glycogen, cellulose, and chitin are
primary examples of polysaccharides.
Starch is the stored form of sugars in plants and is made up of a mixture of
amylose and amylopectin (both polymers of glucose). Plants are able to
synthesize glucose, and the excess glucose, beyond the plant’s immediate
energy needs, is stored as starch in different plant parts, including roots and
seeds. The starch in the seeds provides food for the embryo as it germinates
and can also act as a source of food for humans and animals. The starch that
is consumed by humans is broken down by enzymes, such as salivary
amylases, into smaller molecules, such as maltose and glucose. The cells
can then absorb the glucose.
Starch is made up of glucose monomers that are joined by a 1-4 or a 1-6
glycosidic bonds. The numbers 1-4 and 1-6 refer to the carbon number of
the two residues that have joined to form the bond. As illustrated in [link],
amylose is starch formed by unbranched chains of glucose monomers (only
a 1-4 linkages), whereas amylopectin is a branched polysaccharide (a 1-6
linkages at the branch points).
Amylopectin
Amylose and amylopectin are two different
forms of starch. Amylose is composed of
unbranched chains of glucose monomers
connected by a 1,4 glycosidic linkages.
Amylopectin is composed of branched
chains of glucose monomers connected by a
1,4 and a 1,6 glycosidic linkages. Because
of the way the subunits are joined, the
glucose chains have a helical structure.
Glycogen (not shown) is similar in structure
to amylopectin but more highly branched.
Glycogen is the storage form of glucose in humans and other vertebrates
and is made up of monomers of glucose. Glycogen is the animal equivalent
of starch and is a highly branched molecule usually stored in liver and
muscle cells. Whenever blood glucose levels decrease, glycogen is broken
down to release glucose in a process known as glycogenolysis.
Cellulose is the most abundant natural biopolymer. The cell wall of plants
is mostly made of cellulose; this provides structural support to the cell.
Wood and paper are mostly cellulosic in nature. Cellulose is made up of
glucose monomers that are linked by f 1-4 glycosidic bonds ((link]).
Cellulose fibers
Cellulose structure
H OH CH,OH H OH
HO H H fe) H
fe)
OH H
fe)
H H H
O lo)
CH,OH H OH CH,OH
In cellulose, glucose monomers are
linked in unbranched chains by f 1-4
glycosidic linkages. Because of the
way the glucose subunits are joined,
every glucose monomer is flipped
relative to the next one resulting ina
linear, fibrous structure.
As shown in [link], every other glucose monomer in cellulose is flipped
over, and the monomers are packed tightly as extended long chains. This
gives cellulose its rigidity and high tensile strength—which is so important
to plant cells. While the 6 1-4 linkage cannot be broken down by human
digestive enzymes, herbivores such as cows, koalas, buffalos, and horses
are able, with the help of the specialized flora in their stomach, to digest
plant material that is rich in cellulose and use it as a food source. In these
animals, certain species of bacteria and protists reside in the rumen (part of
the digestive system of herbivores) and secrete the enzyme cellulase. The
appendix of grazing animals also contains bacteria that digest cellulose,
giving it an important role in the digestive systems of ruminants. Cellulases
can break down cellulose into glucose monomers that can be used as an
energy source by the animal. Termites are also able to break down cellulose
because of the presence of other organisms in their bodies that secrete
cellulases.
Carbohydrates serve various functions in different animals. Arthropods
(insects, crustaceans, and others) have an outer skeleton, called the
exoskeleton, which protects their internal body parts (as seen in the bee in
[link]). This exoskeleton is made of the biological macromolecule chitin,
which is a polysaccharide-containing nitrogen. It is made of repeating units
of N-acetyl-6-d-glucosamine, a modified sugar. Chitin is also a major
component of fungal cell walls; fungi are neither animals nor plants and
form a kingdom of their own in the domain Eukarya.
Insects have a hard outer
exoskeleton made of chitin, a type
of polysaccharide. (credit: Louise
Docker)
Benefits of Carbohydrates
Are carbohydrates good for you? People who wish to lose weight are often
told that carbohydrates are bad for them and should be avoided. Some diets
completely forbid carbohydrate consumption, claiming that a low-
carbohydrate diet helps people to lose weight faster. However,
carbohydrates have been an important part of the human diet for thousands
of years; artifacts from ancient civilizations show the presence of wheat,
rice, and corn in our ancestors’ storage areas.
Carbohydrates should be supplemented with proteins, vitamins, and fats to
be parts of a well-balanced diet. Calorie-wise, a gram of carbohydrate
provides 4.3 Kcal. For comparison, fats provide 9 Kcal/g, a less desirable
ratio. Carbohydrates contain soluble and insoluble elements; the insoluble
part is known as fiber, which is mostly cellulose. Fiber has many uses; it
promotes regular bowel movement by adding bulk, and it regulates the rate
of consumption of blood glucose. Fiber also helps to remove excess
cholesterol from the body: fiber binds to the cholesterol in the small
intestine, then attaches to the cholesterol and prevents the cholesterol
particles from entering the bloodstream, and then cholesterol exits the body
via the feces. Fiber-rich diets also have a protective role in reducing the
occurrence of colon cancer. In addition, a meal containing whole grains and
vegetables gives a feeling of fullness. As an immediate source of energy,
glucose is broken down during the process of cellular respiration, which
produces ATP, the energy currency of the cell. Without the consumption of
carbohydrates, the availability of “instant energy” would be reduced.
Eliminating carbohydrates from the diet is not the best way to lose weight.
A low-calorie diet that is rich in whole grains, fruits, vegetables, and lean
meat, together with plenty of exercise and plenty of water, is the more
sensible way to lose weight.
Lipids
Introduction
"A story about the Jack Spratts of medicine [was] told recently by Dr.
Charles H. Best, co-discoverer of insulin. He had been invited to a
conference of heart specialists in North America. On the eve of the meeting,
out of respect for the fat-clogs-the-arteries theory, the delegates sat down to
a special banquet served without fats. It was unpalatable but they all ate it
as a duty. Next morning Best looked round the breakfast room and saw
these same specialists — all in the 40-60 year old, coronary age group —
happily tucking into eggs, bacon, buttered toast and coffee with cream."
Richard Mackarness, Objections To High-Fat Diets’, Eat Fat And Grow
Slim, chapter 3, 1958
Lipids include a diverse group of compounds, including those tasty fats in
your diet, that are largely nonpolar in nature. This is because they are
hydrocarbons that include mostly nonpolar carbon—carbon or carbon—
hydrogen bonds. Non-polar molecules are hydrophobic (“water fearing”),
or insoluble in water. Lipids perform many different functions in a cell.
Cells store energy for long-term use in the form of fats. Lipids also provide
insulation from the environment for plants and animals ({link]). For
example, they help keep aquatic birds and mammals dry when forming a
protective layer over fur or feathers because of their water-repellant
hydrophobic nature. Lipids are also the building blocks of many hormones
and are an important constituent of all cellular membranes. Lipids include
fats, oils, waxes, phospholipids, and steroids.
Hydrophobic lipids in the fur
of aquatic mammals, such as
this river otter, protect them
from the elements. (credit:
Ken Bosma)
Fats and Oils
A fat molecule consists of two main components—glycerol and fatty acids.
Glycerol is an organic compound (alcohol) with three carbons, five
hydrogens, and three hydroxyl (OH) groups. Fatty acids have a long chain
of hydrocarbons to which a carboxyl group is attached, hence the name
“fatty acid.” The number of carbons in the fatty acid may range from 4 to
36; most common are those containing 12—18 carbons. In a fat molecule,
the fatty acids are attached to each of the three carbons of the glycerol
molecule with an ester bond through an oxygen atom ((link]).
Glycerol
Fatty Acid
|
Triacylglycerol
Triacylglycerol is formed by the joining of three
fatty acids to a glycerol backbone in a
condensation reaction. Three molecules of water
are released in the process.
During this ester bond formation, three water molecules are released. The
three fatty acids in the triacylglycerol may be similar or dissimilar. Fats are
also called triacylglycerols or triglycerides because of their chemical
structure. Some fatty acids have common names that specify their origin.
For example, palmitic acid, a saturated fatty acid, is derived from the
palm tree. Arachidic acid is derived from Arachis hypogea, the scientific
name for groundnuts or peanuts.
Fatty acids may be saturated or unsaturated. In a fatty acid chain, if there
are only single bonds between neighboring carbons in the hydrocarbon
chain, the fatty acid is said to be saturated. Saturated fatty acids are
saturated with hydrogen; in other words, the number of hydrogen atoms
attached to the carbon skeleton is maximized. Stearic acid is an example of
a saturated fatty acid ({Llink])
Stearic acid is a common saturated fatty acid.
When the hydrocarbon chain contains a double bond, the fatty acid is said
to be unsaturated. Oleic acid is an example of an unsaturated fatty acid
({link]).
Oleic acid is a common unsaturated fatty acid.
Most unsaturated fats are liquid at room temperature and are called oils. If
there is one double bond in the molecule, then it is known as a
monounsaturated fat (e.g., olive oil), and if there is more than one double
bond, then it is known as a polyunsaturated fat (e.g., canola oil).
When a fatty acid has no double bonds, it is known as a saturated fatty acid
because no more hydrogen may be added to the carbon atoms of the chain.
A fat may contain similar or different fatty acids attached to glycerol. Long
straight fatty acids with single bonds tend to get packed tightly and are solid
at room temperature. Animal fats with stearic acid and palmitic acid
(common in meat) and the fat with butyric acid (common in butter) are
examples of saturated fats. Mammals store fats in specialized cells called
adipocytes, where globules of fat occupy most of the cell’s volume. In
plants, fat or oil is stored in many seeds and is used as a source of energy
during seedling development. Unsaturated fats or oils are usually of plant
origin and contain cis unsaturated fatty acids. Cis and trans indicate the
configuration of the molecule around the double bond. If hydrogens are
present in the same plane, it is referred to as a cis fat; if the hydrogen atoms
are on two different planes, it is referred to as a trans fat. The cis double
bond causes a bend or a “kink” that prevents the fatty acids from packing
tightly, keeping them liquid at room temperature ((link]). Olive oil, corn oil,
canola oil, and cod liver oil are examples of unsaturated fats. Unsaturated
fats help to lower blood cholesterol levels whereas saturated fats contribute
to plaque formation in the arteries.
Saturated fatty acid
Stearic acid
Unsaturated fatty acids
Cis oleic acid
Trans oleic acid
Saturated fatty acids have hydrocarbon chains connected
by single bonds only. Unsaturated fatty acids have one or
more double bonds. Each double bond may be in a cis or
trans configuration. In the cis configuration, both
hydrogens are on the same side of the hydrocarbon
chain. In the trans configuration, the hydrogens are on
opposite sides. A cis double bond causes a kink in the
chain.
Trans Fats
In the food industry, oils are artificially hydrogenated to make them semi-
solid and of a consistency desirable for many processed food products.
Simply speaking, hydrogen gas is bubbled through oils to solidify them.
During this hydrogenation process, double bonds of the cis- conformation
in the hydrocarbon chain may be converted to double bonds in the trans-
conformation.
Margarine, some types of peanut butter, and shortening are examples of
artificially hydrogenated trans fats. Recent studies have shown that an
increase in trans fats in the human diet may lead to an increase in levels of
low-density lipoproteins (LDL), or “bad” cholesterol, which in turn may
lead to plaque deposition in the arteries, resulting in heart disease. Many
fast food restaurants have recently banned the use of trans fats, and food
labels are required to display the trans fat content.
Omega Fatty Acids
Essential fatty acids are fatty acids required but not synthesized by the
human body. Consequently, they have to be supplemented through ingestion
via the diet. Omega-3 fatty acids (like that shown in [link]) fall into this
category and are one of only two known for humans (the other being
omega-6 fatty acid). These are polyunsaturated fatty acids and are called
omega-3 because the third carbon from the end of the hydrocarbon chain is
connected to its neighboring carbon by a double bond.
Alpha-linolenic acid is an example
of an omega-3 fatty acid. It has
three cis double bonds and, as a
result, a curved shape. For clarity,
the carbons are not shown. Each
singly bonded carbon has two
hydrogens associated with it, also
not shown.
The farthest carbon away from the carboxyl group is numbered as the
omega (@) carbon, and if the double bond is between the third and fourth
carbon from that end, it is known as an omega-3 fatty acid. Nutritionally
important because the body does not make them, omega-3 fatty acids
include alpha-linoleic acid (ALA), eicosapentaenoic acid (EPA), and
docosahexaenoic acid (DHA), all of which are polyunsaturated. Salmon,
trout, and tuna are good sources of omega-3 fatty acids. Research indicates
that omega-3 fatty acids reduce the risk of sudden death from heart attacks,
reduce triglycerides in the blood, lower blood pressure, and prevent
thrombosis by inhibiting blood clotting. They also reduce inflammation,
and may help reduce the risk of some cancers in animals.
Like carbohydrates, fats have received a lot of bad publicity. It is true that
eating an excess of fried foods and other “fatty” foods leads to weight gain.
However, fats do have important functions. Many vitamins are fat soluble,
and fats serve as a long-term storage form of fatty acids: a source of energy.
They also provide insulation for the body. Therefore, “healthy” fats in
moderate amounts should be consumed on a regular basis.
Waxes
Wax covers the feathers of some aquatic birds and the leaf surfaces of some
plants. Because of the hydrophobic nature of waxes, they prevent water
from sticking on the surface ([link]). Waxes are made up of long fatty acid
chains esterified to long-chain alcohols.
Waxy coverings on some leaves
are made of lipids. (credit: Roger
Griffith)
Phospholipids
Phospholipids are major constituents of the plasma membrane, the
outermost layer of animal cells. Like fats, they are composed of fatty acid
chains attached to a glycerol or sphingosine backbone. Instead of three fatty
acids attached as in triglycerides, however, there are two fatty acids forming
diacylglycerol, and the third carbon of the glycerol backbone is occupied by
a modified phosphate group ([link]). A phosphate group alone attached to a
diaglycerol does not qualify as a phospholipid; it is phosphatidate
(diacylglycerol 3-phosphate), the precursor of phospholipids. The
phosphate group is modified by an alcohol. Phosphatidylcholine and
phosphatidylserine are two important phospholipids that are found in
plasma membranes.
Phosphate
Hydrophilic head
Saturated
fatty acid
Unsaturated
fatty acid
Hydrophobic tails
A phospholipid is a molecule with
two fatty acids and a modified
phosphate group attached to a
glycerol backbone. The phosphate
may be modified by the addition
of charged or polar chemical
groups. Two chemical groups that
may modify the phosphate,
choline and serine, are shown
here. Both choline and serine
attach to the phosphate group at
the position labeled R via the
hydroxyl group indicated in green.
A phospholipid is an amphipathic molecule, meaning it has a hydrophobic
and a hydrophilic part. The fatty acid chains are hydrophobic and cannot
interact with water, whereas the phosphate-containing group is hydrophilic
and interacts with water ((link]).
nnngeeen Phospholipid
bilayer
Hydrophobic tail
Hydrophilic head group
The phospholipid bilayer is the
major component of all cellular
membranes. The hydrophilic head
groups of the phospholipids face
the aqueous solution. The
hydrophobic tails are sequestered
in the middle of the bilayer.
The head is the hydrophilic part, and the tail contains the hydrophobic fatty
acids. In a membrane, a bilayer of phospholipids forms the matrix of the
structure, the fatty acid tails of phospholipids face inside, away from water,
whereas the phosphate group faces the outside, aqueous side ([link]).
Phospholipids are responsible for the dynamic nature of the plasma
membrane. If a drop of phospholipids is placed in water, it spontaneously
forms a structure known as a micelle, where the hydrophilic phosphate
heads face the outside and the fatty acids face the interior of this structure.
Steroids
Unlike the phospholipids and fats discussed earlier, steroids have a fused
ring structure. Although they do not resemble the other lipids, they are
grouped with them because they are also hydrophobic and insoluble in
water. All steroids have four linked carbon rings and several of them, like
cholesterol, have a short tail (({link]). Many steroids also have the -OH
functional group, which puts them in the alcohol classification (sterols).
Cholesterol
Cortisol
Steroids such as cholesterol and
cortisol are composed of four
fused hydrocarbon rings.
Cholesterol is the most common steroid. Cholesterol is mainly synthesized
in the liver and is the precursor to many steroid hormones such as
testosterone and estradiol, which are secreted by the gonads and endocrine
glands. It is also the precursor to Vitamin D. Cholesterol is also the
precursor of bile salts, which help in the emulsification of fats and their
subsequent absorption by cells. Although cholesterol is often spoken of in
negative terms by lay people, it is necessary for proper functioning of the
body. It is a component of the plasma membrane of animal cells and is
found within the phospholipid bilayer. Being the outermost structure in
animal cells, the plasma membrane is responsible for the transport of
materials and cellular recognition and it is involved in cell-to-cell
communication.
Components and Structure of Plasmal Membranes
Introduction
"The American Heritage Dictionary defines a membrane as a 'thin pliable
layer of plant or animal tissue covering or separating structures or organs’.
The impression this description leaves is one of the plastic wrap covering a
hamburger. By this definition, membranes are static, tough, impenetrable,
and visible. Yet, nothing could be further from the truth. The entire concept
of dynamic behavior is missing from this definition, yet dynamics is what
makes membranes both essential for life and so difficult to study." William
Stillwell, An Introduction to Biological Membranes: From Bilayers to
Rafts, pg. 1, 2013
A cell’s plasma membrane defines the cell, outlines its borders, and
determines the nature of its interaction with its environment. As Stillwell
says above, without membranes there would be no life; they are as essential
to life as DNA or proteins. Cells exclude some substances, take in others,
and excrete still others, all in controlled quantities. The plasma membrane
must be very flexible to allow certain cells, such as red blood cells and
white blood cells, to change shape as they pass through narrow capillaries.
These are the more obvious functions of a plasma membrane. In addition,
the surface of the plasma membrane carries markers that allow cells to
recognize one another, which is vital for tissue and organ formation during
early development, and which later plays a role in the “self” versus “non-
self” distinction of the immune response.
Among the most sophisticated functions of the plasma membrane is the
ability to transmit signals by means of complex, integral proteins known as
membrane receptors. These proteins (and occasionally, lipids) act both as
receivers of extracellular inputs and as activators of intracellular processes.
These membrane receptors provide extracellular attachment sites for
effectors like hormones and growth factors, and they activate intracellular
response cascades when their effectors are bound. Occasionally, receptors
are hijacked by viruses (HIV, human immunodeficiency virus, is one
example) that use them to gain entry into cells, and at times, the genes
encoding receptors become mutated, causing the process of signal
transduction to malfunction with disastrous consequences.
Fluid Mosaic Model
The existence of the plasma membrane was identified in the 1890s, and its
chemical components were identified in 1915. The principal components
identified at that time were lipids and proteins. The first widely accepted
model of the plasma membrane’s structure was proposed in 1935 by Hugh
Davson and James Danielli; it was based on the “railroad track” appearance
of the plasma membrane in early electron micrographs. They theorized that
the structure of the plasma membrane resembles a sandwich, with protein
being analogous to the bread, and lipids being analogous to the filling. In
the 1950s, advances in microscopy, notably transmission electron
microscopy (TEM), allowed researchers to see that the core of the plasma
membrane consisted of a double, rather than a single, layer. A new model
that better explains both the microscopic observations and the function of
that plasma membrane was proposed by S.J. Singer and Garth L. Nicolson
in 1972.
The explanation proposed by Singer and Nicolson, and based on the work
of many others such as Harden McConnell, is called the fluid mosaic
model. The model has evolved somewhat over time, but it still best
accounts for the structure and functions of the plasma membrane as we now
understand them. The fluid mosaic model describes the structure of the
plasma membrane as a mosaic of components—including phospholipids,
cholesterol, proteins, and carbohydrates—that gives the membrane a fluid
character. Plasma membranes range from 5 to 10 nm in thickness. For
comparison, human red blood cells, visible via light microscopy, are
approximately 8 pm wide, or approximately 1,000 times wider than a
plasma membrane. The membrane does look a bit like a sandwich ([link]).
Glycoprotein: protein with Glycolipid: lipid with
[ carbohydrate attached fi carbohydrate
attached
Peripheral membrane Phospholipid
protein bilayer
Cholesterol :
Integral membrane Protein channel
protein
Cytoskeletal filaments
The fluid mosaic model of the plasma membrane describes the
plasma membrane as a fluid combination of phospholipids,
cholesterol, and proteins. Carbohydrates attached to lipids
(glycolipids) and to proteins (glycoproteins) extend from the
outward-facing surface of the membrane.
The principal components of a plasma membrane are lipids (phospholipids
and cholesterol), proteins, and carbohydrates attached to some of the lipids
and some of the proteins. A phospholipid is a molecule consisting of
glycerol, two fatty acids, and a phosphate-linked head group. Cholesterol,
another lipid composed of four fused carbon rings, is found alongside the
phospholipids in the core of the membrane. The proportions of proteins,
lipids, and carbohydrates in the plasma membrane vary with cell type, but
for a typical human cell, protein accounts for about 50 percent of the
composition by mass, lipids (of all types) account for about 40 percent of
the composition by mass, with the remaining 10 percent of the composition
by mass being carbohydrates. However, the concentration of proteins and
lipids varies with different biological membranes. For example, myelin, an
outgrowth of the membrane of specialized cells that insulates the axons of
the peripheral nerves, contains only 18 percent protein and 76 percent lipid.
The mitochondrial inner membrane contains 76 percent protein and only 24
percent lipid. The plasma membrane of human red blood cells is 30 percent
lipid. Carbohydrates are present only on the exterior surface of the plasma
membrane and are attached to proteins, forming glycoproteins, or attached
to lipids, forming glycolipids.
Phospholipids
The main fabric of the membrane is composed of amphiphilic, phospholipid
molecules. The hydrophilic or “water-loving” areas of these molecules
(which look like a collection of balls in an artist’s rendition of the model)
({link]) are in contact with the aqueous fluid both inside and outside the
cell. Hydrophobic, or water-hating molecules, tend to be non-polar. They
interact with other non-polar molecules in chemical reactions, but generally
do not interact with polar molecules. When placed in water, hydrophobic
molecules tend to form a ball or cluster. The hydrophilic regions of the
phospholipids tend to form hydrogen bonds with water and other polar
molecules on both the exterior and interior of the cell. Thus, the membrane
surfaces that face the interior and exterior of the cell are hydrophilic. In
contrast, the interior of the plasma membrane is hydrophobic and will not
interact with water. Therefore, phospholipids form an excellent two-layer
biological membrane that separates fluid within the cell from the fluid
outside of the cell.
A phospholipid molecule ([link]) consists of a three-carbon glycerol
backbone with two fatty acid molecules attached to carbons 1 and 2, anda
phosphate-containing group attached to the third carbon. This arrangement
gives the overall molecule an area described as its head (the phosphate-
containing group), which has a polar character or negative charge, and an
area called the tail (the fatty acids), which has no charge. The head can form
hydrogen bonds, but the tail cannot. A molecule with this arrangement of a
positively or negatively charged area and an uncharged, or non-polar, area
is referred to as amphiphilic or “dual-loving.”
Phosphate
Glycerol
Hydrophilic head
Saturated
fatty acid
Unsaturated
fatty acid
Hydrophobic tails
This phospholipid molecule is
composed of a hydrophilic head
and two hydrophobic tails. The
hydrophilic head group consists of
a phosphate-containing group
attached to a glycerol molecule.
The hydrophobic tails, each
containing either a saturated or an
unsaturated fatty acid, are long
hydrocarbon chains.
This characteristic is vital to the structure of a plasma membrane because,
in water, phospholipids tend to become arranged with their hydrophobic
tails facing each other and their hydrophilic heads facing out. In this way,
they form a lipid bilayer—a barrier composed of a double layer of
phospholipids that separates the water and other materials on one side of the
barrier from the water and other materials on the other side. In fact,
phospholipids heated in an aqueous solution tend to spontaneously form
small spheres or droplets (called micelles or liposomes), with their
hydrophilic heads forming the exterior and their hydrophobic tails on the
inside ([link]).
Lipid-bilayer sphere
Single-layer lipid sphere
Vatatat-
OPO
\7 \7 \7 —-\rvvowuvoy \/
OOS COSC EDOCOHCOH ECHOES
In an aqueous solution,
phospholipids tend to arrange
themselves with their polar heads
facing outward and their
hydrophobic tails facing inward.
(credit: modification of work by
Mariana Ruiz Villareal)
Proteins
Proteins make up the second major component of plasma membranes.
Integral proteins (some specialized types are called integrins) are, as their
name suggests, integrated completely into the membrane structure, and their
hydrophobic membrane-spanning regions interact with the hydrophobic
region of the the phospholipid bilayer ({link]). Single-pass integral
membrane proteins usually have a hydrophobic transmembrane segment
that consists of 20—25 amino acids. Some span only part of the membrane—
associating with a single layer—while others stretch from one side of the
membrane to the other, and are exposed on either side. Some complex
proteins are composed of up to 12 segments of a single protein, which are
extensively folded and embedded in the membrane ((link]). This type of
protein has a hydrophilic region or regions, and one or several mildly
hydrophobic regions. This arrangement of regions of the protein tends to
orient the protein alongside the phospholipids, with the hydrophobic region
of the protein adjacent to the tails of the phospholipids and the hydrophilic
region or regions of the protein protruding from the membrane and in
contact with the cytosol or extracellular fluid.
Integral membranes proteins may
have one or more alpha-helices that
span the membrane (examples 1
and 2), or they may have beta-
sheets that span the membrane
(example 3). (credit:
“Foobar”/Wikimedia Commons)
Peripheral proteins are found on the exterior and interior surfaces of
membranes, attached either to integral proteins or to phospholipids.
Peripheral proteins, along with integral proteins, may serve as enzymes, as
structural attachments for the fibers of the cytoskeleton, or as part of the
cell’s recognition sites. These are sometimes referred to as “cell-specific”
proteins. The body recognizes its own proteins and attacks foreign proteins
associated with invasive pathogens.
Proteins
Introduction
"The characteristic specific properties of native proteins we attribute to their
uniquely defined configurations. The denatured protein molecule we
consider to be characterized by the absence of a uniquely defined
configuration." Alfred E. Mirsky and Linus Pauling, "On the Structure of
Native, Denatured and Coagulated Proteins", Proceedings of the National
Academy of Sciences of the United States of America, 22:442-3, 1936
Proteins are one of the most abundant organic molecules in living systems
and have the most diverse range of functions of all macromolecules. That
diversity of function is due to a tremendous diversity of "uniquely defined"
structures. Proteins may be structural, regulatory, contractile, or protective;
they may serve in transport, storage, or membranes; or they may be toxins
or enzymes. Each cell in a living system may contain thousands of proteins,
each with a unique function. Their structures, like their functions, vary
greatly. They are all, however, polymers of amino acids, arranged in a linear
sequence. But that simple linear sequence is just the beginning of the story.
Types and Functions of Proteins
The primary types and functions of proteins are listed in [link]. We will
consider some of these categories in some detail, but the others will be left
for later discussion.
Enzymes, which are produced by living cells, are catalysts in biochemical
reactions (like digestion) and are usually complex or conjugated proteins.
Each enzyme is specific for the substrate (a reactant that binds to an
enzyme) it acts on. The enzyme may help in breakdown, rearrangement, or
synthesis reactions. Enzymes that break down their substrates are called
catabolic enzymes, and often this is a hydrolysis reaction. Enzymes that
build more complex molecules from their substrates are called anabolic
enzymes, and often this is condensation reaction or dehydration synthesis.
It should be noted that all enzymes increase the rate of reaction and,
therefore, are considered to be organic catalysts. An example of an enzyme
is salivary amylase, which hydrolyzes (breaks down) its substrate amylose,
a component of starch, producing the simple disaccharide known as maltose
along with other simpler sugars. Lastly, most but not all enzymes are
proteins. Some enzymes are composed of RNA (Ribonucleic Acid) or have
RNA components; a topic covered in future chapters.
Hormones are chemical-signaling molecules, usually small proteins or
steroids, secreted by endocrine cells that act to control or regulate specific
physiological processes, including growth, development, metabolism, and
reproduction. For example, insulin is a protein hormone that helps to
regulate the blood glucose level.
Structural proteins are some of the more familiar proteins encountered
everyday. Hair, fingernails, and feathers are largely composed of proteins
called keratins. Your skin contains large quantities of proteins called
collagens and elastins. Other structural proteins are found in bone, in
muscle, in connective tissue, etc.
Storage proteins are used by some organisms to store energy over the long
term, just as carbohydrates and lipids are the preferred energy storage
molecules for other organisms. Casein, a protein found in milk, is one
example. Zein proteins found in wheat grains provide energy for the
developing wheat embryo, but also are critical in helping bread dough to
rise and hold its shape. Egg albumin is an energy source for bird embryonic
development. And proteins found in legumes, such as soybeans and other
beans, nourish the embryos of those plants, as well as billions of humans
around the world.
Protein Types and Functions
Type Examples Functions
Protein Types and Functions
Type
Catabolic/Digestive
Enzymes
Anabolic Enzymes
Transport
Structural
Hormones
Defense
Contractile
Examples
Amylase, lipase,
pepsin, trypsin
DNA
polymerase,
glycogen
synthase
Hemoglobin,
albumin
Actin, tubulin,
keratin, collagen
Insulin, thyroxine
Immunoglobulins
Actin, myosin
Functions
Help in digestion of
food by catabolizing
nutrients into
monomers
Enzymes that make
polymers from
monomers
Carry substances in
the blood or lymph
throughout the body
Compose structures
that support cell
organelles (e.g.
cytoskeleton) or body
parts (e.g. tendons,
cartilage)
Coordinate the
activity of different
body systems
Protect the body from
foreign pathogens
Muscle contraction
Protein Types and Functions
Type Examples Functions
Provide nourishment
in early development
of the embryo and the
seedling
Legume storage
Storage proteins, egg
white (albumin)
Proteins have different shapes and molecular weights; some proteins are
globular in shape whereas others are fibrous in nature. For example,
hemoglobin is a globular protein, but collagen, found in our skin, is a
fibrous protein. Protein shape is critical to its function, and this shape is
maintained by many different types of chemical bonds. Changes in
temperature, pH, salinity and exposure to chemicals may lead to permanent
changes in the shape of the protein, leading to loss of function, known as
denaturation. All proteins are made up of different arrangements of the
same 20 types of amino acids.
Amino Acids
Amino acids are the monomers that make up proteins. Each amino acid has
the same fundamental structure, which consists of a central carbon atom,
also known as the alpha (a) carbon, bonded to an amino group (NH)), a
carboxyl group (COOH), and to a hydrogen atom. Every amino acid also
has another atom or group of atoms bonded to the central atom known as
the R group ([link]).
Amino group Carboxyl group
a carbon
Amino acids have a central
asymmetric carbon to which an
amino group, a carboxyl group, a
hydrogen atom, and a side chain
(R group) are attached.
The name "amino acid" is derived from the fact that they contain both
amino group and carboxyl-acid-group in their basic structure. As
mentioned, there are 20 amino acids present in proteins. Ten of these are
considered essential amino acids in humans because the human body cannot
produce them and they are obtained from the diet. For each amino acid, the
R group (or side chain) is different ({link]).
Coo-
al
H3N—C —H
CH,
CH,
Alanine ee
] 2
= : |
COO NH
Hai—¢ —H ! lees
I *NH3 co NH»
CH, NH,
CH Lysine Arginine Histidine
CHg
CH;
Isoleucine
CH,
|
Ccoo™
Glutamate
Threonine Cysteine COO- COO
: | | |
coo" coo- S| HN HyN—C—H H3N—C—H
I
- | a
H3N—C—H H3N—C—H
|
CH,
|
CH,
|
Fe
HN No
Proline Asparagine Glutamine
gas Phenylalanine Tyrosine Tryptophan
There are 20 common amino acids commonly found in
proteins, each with a different R group (variant group)
that determines its chemical nature.
The chemical nature of the side chain determines the nature of the amino
acid (that is, whether it is acidic, basic, polar, or nonpolar). For example, the
amino acid glycine has a hydrogen atom as the R group. Amino acids such
as valine, methionine, and alanine are nonpolar or hydrophobic in nature,
while amino acids such as serine, threonine, and cysteine are polar and have
hydrophilic side chains. The side chains of lysine and arginine are
positively charged, and therefore these amino acids are also known as basic
amino acids. Proline has an R group that is linked to the amino group,
forming a ring-like structure. Proline is an exception to the standard
structure of an amino acid since its amino group is not separate from the
side chain ([link]).
Amino acids are represented by a single upper case letter or a three-letter
abbreviation. For example, valine is known by the letter V or the three-
letter symbol val. Just as some fatty acids are essential to a diet, some
amino acids are necessary as well. They are known as essential amino
acids, and in humans they include isoleucine, leucine, and cysteine.
Essential amino acids refer to those necessary for construction of proteins in
the body, although not produced by the body; which amino acids are
essential varies from organism to organism.
The sequence and the number of amino acids ultimately determine the
protein's shape, size, and function. Each amino acid is attached to another
amino acid by a covalent bond, known as a peptide bond, which is formed
by a condensation reaction. The carboxyl group of one amino acid and the
amino group of the incoming amino acid combine, releasing a molecule of
water. The resulting bond is the peptide bond ({link]).
Peptide Bond
Peptide bond formation is a
condensation reaction. The
carboxyl group of one amino acid
is linked to the amino group of the
incoming amino acid. In the
process, a molecule of water is
released.
The products formed by such linkages are called peptides. As more amino
acids join to this growing chain, the resulting chain is known as a
polypeptide. Each polypeptide has a free amino group at one end. This end
is called the N terminal, or the amino terminal, and the other end has a free
carboxyl group, also known as the C or carboxy] terminal. While the terms
polypeptide and protein are sometimes used interchangeably, a polypeptide
is technically a polymer of amino acids, whereas the term protein is used
for a polypeptide or polypeptides that have combined together, often have
bound non-peptide prosthetic groups, have a distinct shape, and have a
unique function. After protein synthesis (translation), most proteins are
modified. These are known as post-translational modifications. They may
undergo cleavage, phosphorylation, or may require the addition of other
chemical groups. Only after these modifications is the protein completely
functional.
Note:
Evolution Connection
The Evolutionary Significance of Cytochrome c
Cytochrome c is an important component of the electron transport chain, a
part of cellular respiration, and it is normally found in the cellular
organelle, the mitochondrion. This protein has a heme prosthetic group,
and the central ion of the heme gets alternately reduced and oxidized
during electron transfer. Because this essential protein’s role in producing
cellular energy is crucial, it has changed very little over millions of years.
Protein sequencing has shown that there is a considerable amount of
cytochrome c amino acid sequence homology among different species; in
other words, evolutionary kinship can be assessed by measuring the
similarities or differences among various species’ DNA or protein
sequences.
Scientists have determined that human cytochrome c contains 104 amino
acids. For each cytochrome c molecule from different organisms that has
been sequenced to date, 37 of these amino acids appear in the same
position in all samples of cytochrome c. This indicates that there may have
been a common ancestor. On comparing the human and chimpanzee
protein sequences, no sequence difference was found. When human and
rhesus monkey sequences were compared, the single difference found was
in one amino acid. In another comparison, human to yeast sequencing
shows a difference in the 44th position.
Protein Structure
As discussed earlier, the shape of a protein is critical to its function. For
example, an enzyme can bind to a specific substrate at a site known as the
active site. If this active site is altered because of local changes or changes
in overall protein structure, the enzyme may be unable to bind to the
substrate. To understand how the protein gets its final shape or
conformation, we need to understand the four levels of protein structure:
primary, secondary, tertiary, and quaternary.
Primary Structure
The unique sequence of amino acids in a polypeptide chain is its primary
structure. For example, the pancreatic hormone insulin has two
polypeptide chains, A and B, and they are linked together by disulfide
bonds. The N terminal amino acid of the A chain is glycine, whereas the C
terminal amino acid is asparagine ({link]). The sequences of amino acids in
the A and B chains are unique to insulin.
Bovine serum insulin is a protein hormone made
of two peptide chains, A (21 amino acids long) and
B (30 amino acids long). In each chain, primary
structure is indicated by three-letter abbreviations
that represent the names of the amino acids in the
order they are present. The amino acid cysteine
(cys) has a sulfhydryl (SH) group as a side chain.
Two sulfhydryl groups can react in the presence of
oxygen to form a disulfide (S-S) bond. Two
disulfide bonds connect the A and B chains
together, and a third helps the A chain fold into the
correct shape. Note that all disulfide bonds are the
same length, but are drawn different sizes for
clarity.
The unique sequence for every protein is ultimately determined by the gene
encoding the protein. A change in nucleotide sequence of the gene’s coding
region may lead to a different amino acid being added to the growing
polypeptide chain, causing a change in protein structure and function. In
sickle cell anemia, the hemoglobin f chain (a small portion of which is
shown in [link]) has a single amino acid substitution, causing a change in
protein structure and function. Specifically, the amino acid glutamic acid is
substituted by valine in the 6 chain. What is most remarkable to consider is
that a hemoglobin molecule is made up of two alpha chains and two beta
chains that each consist of about 150 amino acids. The molecule, therefore,
has about 600 amino acids. The structural difference between a normal
hemoglobin molecule and a sickle cell molecule—which dramatically
decreases life expectancy—is a single amino acid of the 600. What is even
more remarkable is that those 600 amino acids are encoded by three
nucleotides each, and the mutation is caused by a single base change (point
mutation), 1 in 1800 bases.
H H O
ee ee |
threonine — proline —-N —C — O —lys
CH,
| ll
CH, —C — OH
‘ ; Normal
glutamic acid hemoglobin
Amino acid
' ' 7 substitution
threonine — proline —- N —C — 0 ——lys gy
H3c — CH— CH
valine Sickle cell
hemoglobin
The beta chain of hemoglobin is 147
residues in length, yet a single amino
acid substitution leads to sickle cell
anemia. In normal hemoglobin, the
amino acid at position seven is
glutamate. In sickle cell hemoglobin,
this glutamate is replaced by a valine.
Because of this change of one amino acid in the chain, hemoglobin
molecules form long fibers that distort the biconcave, or disc-shaped, red
blood cells and assume a crescent or “sickle” shape, which clogs arteries
({link]). This can lead to myriad serious health problems such as
breathlessness, dizziness, headaches, and abdominal pain for those affected
by this disease.
In this blood smear, visualized at
535x magnification using bright
field microscopy, sickle cells are
crescent shaped, while normal
cells are disc-shaped. (credit:
modification of work by Ed
Uthman; scale-bar data from Matt
Russell)
Secondary Structure
The local folding of the polypeptide in some regions gives rise to the
secondary structure of the protein. The most common are the a-helix and
B-pleated sheet structures ([link]). Both structure types are held in shape by
hydrogen bonds. The hydrogen bonds form between the oxygen atom in the
carbonyl group in one amino acid and another amino acid that is four amino
acids farther along the chain.
a-helix
B-pleated
sheet
oO
QomwR HoeQummR Ho HeQuemi HieQuem 1
1 toa i) | i ie i] I
C7ESN=C AC LN=C7ESN=C AG DN-C7ESN=C uc LN=C7ESN=C AG N-C
eal 1 1ot I (a 1 io
HH R HHO " Bee 6
The a-helix and B-pleated sheet are
secondary structures of proteins that form
because of hydrogen bonding between
carbonyl and amino groups in the peptide
backbone. Certain amino acids have a
propensity to form an a-helix, while others
have a propensity to form a f-pleated sheet.
Every helical turn in an alpha helix has 3.6 amino acid residues. The R
groups (the variant groups) of the polypeptide protrude out from the a-helix
chain. In the B-pleated sheet, the “pleats” are formed by hydrogen bonding
between atoms on the backbone of the polypeptide chain. The R groups are
attached to the carbons and extend above and below the folds of the pleat.
The pleated segments align parallel or antiparallel to each other, and
hydrogen bonds form between the partially positive nitrogen atom in the
amino group and the partially negative oxygen atom in the carbonyl group
of the peptide backbone. The a-helix and B-pleated sheet structures are
found in most globular and fibrous proteins and they play an important
structural role.
Tertiary Structure
The unique three-dimensional structure of a polypeptide is its tertiary
structure ({link]). This structure is in part due to chemical interactions at
work on the polypeptide chain. Primarily, the interactions among R groups
creates the complex three-dimensional tertiary structure of a protein. The
nature of the R groups found in the amino acids involved can counteract the
formation of the hydrogen bonds described for standard secondary
structures. For example, R groups with like charges are repelled by each
other and those with unlike charges are attracted to each other (ionic
bonds). When protein folding takes place, the hydrophobic R groups of
nonpolar amino acids lay in the interior of the protein, whereas the
hydrophilic R groups lay on the outside. The former types of interactions
are also known as hydrophobic interactions. Interaction between cysteine
side chains forms disulfide linkages in the presence of oxygen, the only
covalent bond forming during protein folding.
Polypeptide backbone
ll
CH, — CH, — CH, — CH, — NH3* “O—C— CH,
lonic bond
Dissulfide
linkage
Ss
Ss
Hydrophobic
interactions
The tertiary structure of proteins is determined by a
variety of chemical interactions. These include
hydrophobic interactions, ionic bonding, hydrogen
bonding and disulfide linkages.
All of these interactions, weak and strong, determine the final three-
dimensional shape of the protein. When a protein loses its three-
dimensional shape, it may no longer be functional.
Quaternary Structure
In nature, some proteins are formed from several polypeptides, also known
as subunits, and the interaction of these subunits forms the quaternary
structure. Weak interactions between the subunits help to stabilize the
overall structure. For example, insulin (a globular protein) has a
combination of hydrogen bonds and disulfide bonds that cause it to be
mostly clumped into a ball shape. Insulin starts out as a single polypeptide
and loses some internal sequences in the presence of post-translational
modification after the formation of the disulfide linkages that hold the
remaining chains together. Silk (a fibrous protein), however, has a B-pleated
sheet structure that is the result of hydrogen bonding between different
chains.
The four levels of protein structure (primary, secondary, tertiary, and
quatemary) are illustrated in [link].
Amino acids
Primary Protein structure
sequence of a chain of
animo acids
Pleated sheet 422 Alpha helix
Pleated sheet Tertiary protein structure
three-dimensional folding
pattern of a protein due to side
chain interactions
Alpha helix
g
Quaternary protein structure
protein consisting of more
than one amino acid chain
The four levels of protein structure can be
observed in these illustrations. (credit:
modification of work by National Human Genome
Research Institute)
Secondary Protein structure
hydrogen bonding of the peptide
backbone causes the amino
acids to fold into a repeating
pattern
NAP
Denaturation and Protein Folding
Each protein has its own unique sequence and shape that are held together
by chemical interactions (covalent, ionic and hydrogen bonds). As noted by
Mirsky and Pauling in the epigraph above, a denatured protein is one that
has lost that unique shape and configuration. If the protein is subject to
changes in temperature, pH, salinity or exposure to chemicals, the protein
structure may change, losing its shape without losing its primary sequence
in what is known as denaturation. During denaturation, the changes in the
environment surrounding the protein alter the chemical interactions (ionic
and hydrogen bonds) within the protein causing changes in the shape and
configuration of that protein. Denaturation may be reversible because the
primary structure of the polypeptide is conserved in the process if the
denaturing agent is removed, allowing the protein to resume its function.
However, denaturation is often irreversible, leading to loss of function. One
example of irreversible protein denaturation is when an egg is fried. The
albumin protein in the liquid egg white is denatured when placed in a hot
pan. Not all proteins are denatured at high temperatures; for instance,
bacteria that survive in hot springs have proteins that function at
temperatures close to boiling. The stomach is also very acidic, has a low
pH, and denatures proteins as part of the digestion process; however, the
digestive enzymes of the stomach retain their activity under these
conditions.
Protein folding is critical to its function. It was originally thought that the
proteins themselves were responsible for the folding process. Only recently
was it found that often they receive assistance in the folding process from
protein helpers known as chaperones (or chaperonins) that associate with
the target protein during the folding process. They act by preventing
aggregation of polypeptides that make up the complete protein structure,
and they disassociate from the protein once the target protein is folded.
Enzymes
"Yet even after Galileo and Newton, there remained another question: Were
living things somehow different from rocks and water and stars? Did
animate and inanimate matter differ in some fundamental way? the
"vitalists" claimed that animate matter had some special essence, an
intangible spirit or soul, while the "mechanists" argued that living things
were elaborate machines and obeyed precisely the same laws of physics and
chemistry as did inanimate material. " Alan Lightman, "Our Place in the
Universe", Harper's Magazine, December 2012.
One of the greatest scientists of all time, Louis Pasteur, believed that
metabolic reactions such as fermentation could only occur in living cells.
This perspective was widely shared by scientists of the 19th Century. Thus
one of the first damaging blows to the vitalist perspective came in the late
19th Century, when Eduard Buchner showed that a cell-free extract from
yeast could carry out the synthesis of ethanol from glucose (alcoholic
fermentation). Whole cells were not required for this process. These
extracts were called "enzymes", which derives from the Greek words "en"
(in) + "zyme" (yeast). Buchner demonstrated that there was something "in
yeast", as opposed to the yeast cells themselves, that could convert glucose
to ethanol. The subsequent work of many other scientists has built on this
simple concept - cells contain substances that catalyze reactions, and these
substances can be studied apart from the cells themselves.
A substance that helps a chemical reaction to occur is a catalyst, and the
special molecules that catalyze biochemical reactions are called enzymes.
Almost all enzymes are proteins, made up of chains of amino acids, and
they perform the critical task of lowering the activation energies of
chemical reactions inside the cell. Enzymes do this by binding to the
reactant molecules, and holding them in such a way as to make the
chemical bond-breaking and bond-forming processes take place more
readily. It is important to remember that enzymes don’t change the AG of a
reaction. In other words, they don’t change whether a reaction is exergonic
(spontaneous) or endergonic. This is because they don’t change the free
energy of the reactants or products. They only reduce the activation energy
required to reach the transition state ({link]).
Activation
energy
Activation (Y>x)
energy products
(XY)
Enzymes lower the activation
energy of the reaction but do
not change the free energy of
the reaction.
Enzyme Active Site and Substrate Specificity
The chemical reactants to which an enzyme binds are the enzyme’s
substrates. There may be one or more substrates, depending on the
particular chemical reaction. In some reactions, a single-reactant substrate is
broken down into multiple products. In others, two substrates may come
together to create one larger molecule. Two reactants might also enter a
reaction, both become modified, and leave the reaction as two products.
The location within the enzyme where the substrate binds is called the
enzyme’s active site. The active site is where the “action” happens, so to
speak. Since enzymes are proteins, there is a unique combination of amino
acid residues (also called side chains, or R groups) within the active site.
Each residue is characterized by different properties. Residues can be large
or small, weakly acidic or basic, hydrophilic or hydrophobic, positively or
negatively charged, or neutral. The unique combination of amino acids,
their positions, sequences, structures, and properties, creates a very specific
chemical environment within the active site. This specific environment is
suited to bind, albeit briefly, to a specific chemical substrate (or substrates).
Due to this jigsaw puzzle-like match between an enzyme and its substrates
(which adapts to find the best fit between the transition state and the active
site), enzymes are known for their specificity. The “best fit” results from the
shape and the amino acid functional group’s attraction to the substrate.
There is a specifically matched enzyme for each substrate and, thus, for
each chemical reaction; however, there is flexibility as well.
Environmental factors influence enzyme activity
The fact that active sites are so perfectly suited to provide specific
environmental conditions also means that they are subject to influences by
the local environment. The environmental conditions can include
temperature, pH, salinity and presence of heavy metals. It is true that
increasing the environmental temperature generally increases reaction rates,
enzyme-catalyzed or otherwise. However, increasing or decreasing the
temperature outside of an optimal range can affect chemical bonds within
the active site in such a way that they are less well suited to bind substrates.
High temperatures will eventually cause enzymes, like other biological
molecules, to denature, a process that changes the natural properties of a
substance. Likewise, the pH of the local environment can also affect
enzyme function. Active site amino acids have their own acidic or basic
properties that are optimal for catalysis. These amino acids are sensitive to
changes in pH that can impair the way substrate molecules bind. Enzymes
are suited to function best within a certain pH range, and, as with
temperature, extreme pH values (acidic or basic) of the environment can
cause enzymes to denature an the rates of the reaction decrease ([link]).
Rate of reaction
10 30 50 70 2 4 6 8 10
Temperature (°C) pH
The effects of temperature and pH on the rate
of enzyme catalyzed reaction.
Induced Fit and Enzyme Function
For many years, scientists thought that enzyme-substrate binding took place
in a simple “lock-and-key” fashion. This model asserted that the enzyme
and substrate fit together perfectly in one instantaneous step. However,
current research supports a more refined view called induced fit ((link]).
The induced-fit model expands upon the lock-and-key model by describing
a more dynamic interaction between enzyme and substrate. As the enzyme
and substrate come together, their interaction causes a mild shift in the
enzyme’s structure that confirms an ideal binding arrangement between the
enzyme and the transition state of the substrate. This ideal binding
maximizes the enzyme’s ability to catalyze its reaction.
When an enzyme binds its substrate, an enzyme-substrate complex is
formed. This complex lowers the activation energy of the reaction and
promotes its rapid progression in one of many ways. On a basic level,
enzymes promote chemical reactions that involve more than one substrate
by bringing the substrates together in an optimal orientation. The
appropriate region (atoms and bonds) of one molecule is juxtaposed to the
appropriate region of the other molecule with which it must react. Another
way in which enzymes promote the reaction of their substrates is by
creating an optimal environment within the active site for the reaction to
occur. Certain chemical reactions might proceed best in a slightly acidic or
non-polar environment. The chemical properties that emerge from the
particular arrangement of amino acid residues within an active site create
the perfect environment for an enzyme’s specific substrates to react.
You’ve learned that the activation energy required for many reactions
includes the energy involved in manipulating or slightly contorting
chemical bonds so that they can easily break and allow others to reform.
Enzymatic action can aid this process. The enzyme-substrate complex can
lower the activation energy by contorting substrate molecules in such a way
as to facilitate bond-breaking, helping to reach the transition state. Finally,
enzymes can also lower activation energies by taking part in the chemical
reaction itself. The amino acid residues can provide certain ions or chemical
groups that actually form covalent bonds with substrate molecules as a
necessary step of the reaction process. In these cases, it is important to
remember that the enzyme will always return to its original state at the
completion of the reaction. One of the hallmark properties of enzymes is
that they remain ultimately unchanged by the reactions they catalyze. After
an enzyme is done catalyzing a reaction, it releases its product(s).
Enzyme changes shape
Substrate slightly as substrate binds
Active site
(2
@ »
y
W, 2
= = =
Substrate entering Enzyme/substrate Enzyme/products Products leaving
active site of enzyme complex complex active site of enzyme
According to the induced-fit model, both enzyme and
substrate undergo dynamic conformational changes upon
binding. The enzyme contorts the substrate into its
transition state, thereby increasing the rate of the
reaction.
Buffers and Enzymes
pH and Buffers
The pH of a solution indicates its acidity or alkalinity. The pH scale is, as
previously mentioned, an inverse logarithm and ranges from 0 to 14
({link]). Anything below 7.0 (ranging from 0.0 to 6.9) is acidic, and
anything above 7.0 (from 7.1 to 14.0) is alkaline. Extremes in pH in either
direction from 7.0 are usually considered inhospitable to life. The pH inside
cells (6.8) and the pH in the blood (7.4) are both very close to neutral.
13 Bleach
12 Soapy water
11 Ammonia solution
10 Milk of magnesia
9 Baking soda
8 Sea water
7 Distilled water
6 Urine
5 Black coffee
4 Tomato juice
3 Orange juice
2 Lemon juice
1 Gastric acid
0
The pH scale measures the
concentration of hydrogen
ions (H") in a solution.
(credit: modification of work
by Edward Stevens)
So how can organisms whose bodies require a near-neutral pH ingest acidic
and basic substances (a human drinking orange juice, for example) and
survive? Buffers are the key. Buffers readily absorb excess H* or OH,
keeping the pH of the body carefully maintained in the narrow range
required for survival. Maintaining a constant blood pH is critical to a
person’s well-being. The buffer maintaining the pH of human blood
involves carbonic acid (H»CO3), bicarbonate ion (HCO3_), and carbon
dioxide (CO2). When bicarbonate ions combine with free hydrogen ions
and become carbonic acid, hydrogen ions are removed, moderating pH
changes. Similarly, as shown in [link], excess carbonic acid can be
converted to carbon dioxide gas and exhaled through the lungs. This
prevents too many free hydrogen ions from building up in the blood and
dangerously reducing the blood’s pH. Likewise, if too much OH™ is
introduced into the system, carbonic acid will combine with it to create
bicarbonate, lowering the pH. Without this buffer system, the body’s pH
would fluctuate enough to put survival in jeopardy.
ie HCO3__
This diagram shows the body’s buffering of blood pH
levels. The blue arrows show the process of raising pH
as more CO, is produced and exhaled. The purple
arrows indicate the reverse process: the lowering of
pH as more bicarbonate (HCO3_) is generated from
the CO, being produced by cellular respiration. In
short, when more CO, is exhaled, blood pH goes up
and the blood is more basic, and if CO> is converted to
bicarbonate, blood pH goes down and the blood is
more acidic.
Other examples of buffers are antacids used to combat excess stomach acid.
Many of these over-the-counter medications work in the same way as blood
buffers, usually with at least one ion capable of absorbing hydrogen and
moderating pH, bringing relief to those that suffer “heartburn” after eating.
The unique properties of water that contribute to this capacity to balance pH
—as well as water’s other characteristics—are essential to sustaining life on
Earth.
Enzyme Function and Buffers
On the cellular level, cells need to maintain a relatively constant internal
environment, because many important cellular functions only take place
within a narrow of conditions, such as temperature and pH. Enzymes
function is influenced by the pH of its environment and only function
optimally within a narrow pH range. Losing function of just one enzyme
can mean death for a cell, or tissue, or organ or and entire organism. In
addition, there are many reactions occurring in a cell that either produces or
consumes Hydrogen ions thereby changing the pH of the cells environment.
How do cells maintain pH within the range necessary for enzymes to
function properly? The answer is buffers, just as learned earlier about your
whole body using buffers to maintain its pH.
Nucleic Acids and Nucleotides
"If the results of the present study on the chemical nature of the
transforming principle are confirmed, then nucleic acids must be regarded
as possessing biological specificity, the nature of which is as yet
undetermined." O.T. Avery, C. MacLeod, and M McCarty, "Studies on the
Chemical Nature of the Substance Inducing Transformation of
Pneumococcal Types", Journal of Experimental Medicine 1944, Volume 79,
p;.155:
In 1944, when Avery, MacLeod and McCarty published the work quoted
above, the structure of nucleic acids was still unknown. But their work was
one of the more important bits of evidence indicating that nucleic acids
contained important biological information. We now know a lot more about
the information content, and, thanks to the work of Watson and Crick a few
years after this statement was published, we know how the structure of
nucleic acids is related to the function of information storage, We know that
nucleic acids are the most important macromolecules for the continuity of
life. They carry the genetic blueprint of a cell, and carry instructions for the
functioning of the cell.
DNA and RNA
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and
ribonucleic acid (RNA). DNA is the genetic material found in all living
organisms, ranging from single-celled bacteria to multicellular mammals. It
is found in the nucleus of eukaryotes and in the organelles, chloroplasts, and
mitochondria. In prokaryotes, the DNA is not enclosed in a membranous
envelope.
The entire genetic content of a cell is known as its genome, and the study of
genomes is genomics. In eukaryotic cells but not in prokaryotes, DNA
forms a complex with histone proteins to form chromatin, the substance of
eukaryotic chromosomes. A chromosome may contain tens of thousands of
genes. Many genes contain the information to make protein products; other
genes code for RNA products. DNA controls all of the cellular activities by
turning the genes “on” or “off.”
The other type of nucleic acid, RNA, is mostly involved in protein
synthesis. The DNA molecules never leave the nucleus but instead use an
intermediary to communicate with the rest of the cell. This intermediary is
the messenger RNA (mRNA). Other types of RNA—like rRNA, tRNA,
and microRNA—are involved in protein synthesis and its regulation.
DNA and RNA are made up of monomers known as nucleotides. The
nucleotides combine with each other to form a polynucleotide or nucleic
acid, DNA or RNA. Each nucleotide is made up of three components: a
nitrogenous base, a pentose (five-carbon) sugar, and a phosphate group
({link]). Each nitrogenous base in a nucleotide is attached to a sugar
molecule, which is attached to one or more phosphate groups. Some
nucleotides such as ATP (Adenosine Triphosphate) are a short term energy
source for all cells and is called the "Energy currency of the cell."
Pyrimidines
a or
Ze x we 8 en
— —- DNA) Uracil © RNA)
Purines
=.
H
rt ;
An, af > Nn
eA.
Adenine AEN
A nucleotide is made up of three components: a nitrogenous base, a
pentose sugar, and one or more phosphate groups. Carbon residues in
the pentose are numbered 1’ through 5’ (the prime distinguishes these
residues from those in the base, which are numbered without using a
prime notation). The base is attached to the 1’ position of the ribose,
and the phosphate is attached to the 5’ position. When a
polynucleotide is formed, the 5’ phosphate of the incoming nucleotide
attaches to the 3’ hydroxyl group at the end of the growing chain.
Two types of pentose are found in nucleotides, deoxyribose (found in
DNA) and ribose (found in RNA). Deoxyribose is similar in structure
to ribose, but it has an H instead of an OH at the 2’ position. Bases
can be divided into two categories: purines and pyrimidines. Purines
have a double ring structure, and pyrimidines have a single ring.
The nitrogenous bases, important components of nucleotides, are organic
molecules and are so named because they contain carbon and nitrogen.
They are bases because they contain an amino group that has the potential
of binding an extra hydrogen, and thus, decreases the hydrogen ion
concentration in its environment, making it more basic. Each nucleotide in
DNA contains one of four possible nitrogenous bases: adenine (A), guanine
(G) cytosine (C), and thymine (T).
Adenine and guanine are classified as purines. The primary structure of a
purine is two carbon-nitrogen rings. Cytosine, thymine, and uracil are
classified as pyrimidines which have a single carbon-nitrogen ring as their
primary structure (({link]). Each of these basic carbon-nitrogen rings has
different functional groups attached to it. In molecular biology shorthand,
the nitrogenous bases are simply known by their symbols A, T, G, C, and U.
DNA contains A, T, G, and C whereas RNA contains A, U, G, and C.
The pentose sugar in DNA is deoxyribose, and in RNA, the sugar is ribose
({link]). The difference between the sugars is the presence of the hydroxyl
group on the second carbon of the ribose and hydrogen on the second
carbon of the deoxyribose. The carbon atoms of the sugar molecule are
numbered as 1’, 2’, 3’, 4’, and 5’ (1’ is read as “one prime”). The phosphate
residue is attached to the hydroxyl group of the 5’ carbon of one sugar and
the hydroxyl! group of the 3’ carbon of the sugar of the next nucleotide,
which forms a 5'—3' phosphodiester bond. The phosphodiester bond is not
formed by simple condensation reaction like the other linkages connecting
monomers in macromolecules: its formation involves the removal of two
phosphate groups. A polynucleotide may have thousands of such
phosphodiester bonds.
DNA Double-Helix Structure
DNA has a double-helix structure ([link]). The sugar and phosphate lie on
the outside of the helix, forming the backbone of the DNA. The nitrogenous
bases are stacked in the interior, like the steps of a staircase, in pairs; the
pairs are bound to each other by hydrogen bonds. Every base pair in the
double helivx is separated from the next base pair by 0.34 nm. The two
strands of the helix run in opposite directions, meaning that the 5’ carbon
end of one strand will face the 3’ carbon end of its matching strand. (This is
referred to as antiparallel orientation and is important to DNA replication
and in many nucleic acid interactions.)
Native DNA is an
antiparallel double helix.
The phosphate backbone
(indicated by the curvy
lines) is on the outside,
and the bases are on the
inside. Each base from
one strand interacts via
hydrogen bonding with a
base from the opposing
strand. (credit: Jerome
Walker/Dennis Myts)
Only certain types of base pairing are allowed. For example, a certain
purine can only pair with a certain pyrimidine. This means A can pair with
T, and G can pair with C, as shown in [link]. This is known as the base
complementary rule. In other words, the DNA strands are complementary
to each other. If the sequence of one strand is AATTGGCC, the
complementary strand would have the sequence TTAACCGG. During
DNA replication, each strand is copied, resulting in a daughter DNA double
helix containing one parental DNA strand and a newly synthesized strand.
QO Oo
a on ~~) On
an ----Y Cytosine fe)
HO. Guanine NH2 vt
In a double stranded DNA molecule,
the two strands run antiparallel to one
another so that one strand runs 5’ to 3’
and the other 3’ to 5’. The phosphate
backbone is located on the outside,
and the bases are in the middle.
Adenine forms hydrogen bonds (or
base pairs) with thymine, and guanine
base pairs with cytosine.
RNA
Ribonucleic acid, or RNA, is mainly involved in the process of protein
synthesis under the direction of DNA. RNA is usually single-stranded and
is made of ribonucleotides that are linked by phosphodiester bonds. A
ribonucleotide in the RNA chain contains ribose (the pentose sugar), one of
the four nitrogenous bases (A, U, G, and C), and the phosphate group. The
function of RNA is to make proteins from the information stored on the
DNA.
Features of DNA and RNA
DNA RNA
; Carries genetic Involved in protein
Function ; é ’
information synthesis
Location Remains in the Leaves the nucleus
nucleus
Structure Double helix Usually single-stranded
Features of DNA and RNA
DNA
Sugar Deoxyribose
Pyrimidines Cytosine, thymine
Purines Adenine, guanine
RNA
Ribose
Cytosine, uracil
Adenine, guanine
Cell Reproduction
By the end of this section, you will be able to:
e Describe the structure of prokaryotic and eukaryotic genomes
e Distinguish between chromosomes, genes, and traits
e Describe the mechanisms of chromosome compaction
Introduction
"DNA was the first three-dimensional Xerox machine." Kenneth E.
Boulding, in Richard P. Beilock (ed.), Beasts, Ballads and Bouldingisms: A
Selection of Writings by Kenneth E. Boulding, pg. 160, 1976
Non scientists like Boulding , who was an economist, are fond of using
machines as metaphors for biological structures and functions. But DNA is
a lot more than just a Xerox machine, as you will learn in this section. In
fact, the more we learn about DNA, the more remarkable it seems. For
DNA not only replicates itself, it directs the development, life, and demise
of every organism on the planet.
A sea urchin
begins life
as a single
cell that (a)
divides to
form two
cells, visible
by scanning
electron
microscopy.
After four
rounds of
cell
division, (b)
there are 16
cells, as
seen in this
SEM image.
After many
rounds of
cell
division, the
individual
develops
into a
complex,
multicellula
r organism,
as seen in
this (c)
mature sea
urchin.
(credit a:
modificatio
n of work
by Evelyn
Spiegel,
Louisa
Howard;
credit b:
modificatio
n of work
by Evelyn
Spiegel,
Louisa
Howard;
credit c:
modificatio
n of work
by Marco
Busdraghi;
scale-bar
data from
Matt
Russell)
A human, as well as every sexually reproducing organism, begins life as a
fertilized egg (embryo) or zygote. Trillions of cell divisions subsequently
occur in a controlled manner to produce a complex, multicellular human. In
other words, that original single cell is the ancestor of every other cell in the
body. Once a being is fully grown, cell reproduction is still necessary to
repair or regenerate tissues. For example, new blood and skin cells are
constantly being produced. All multicellular organisms use cell division for
growth and the maintenance and repair of cells and tissues. Cell division is
tightly regulated, and the occasional failure of regulation can have life-
threatening consequences. Single-celled organisms use cell division as their
method of reproduction.
So, the continuity of life from one cell to another has its foundation in the
reproduction of cells by way of the cell cycle. The cell cycle is an orderly
sequence of events that describes the stages of a cell’s life from the division
of a single parent cell to the production of two new daughter cells. The
mechanisms involved in the cell cycle are highly regulated.
Genomic DNA
Before discussing the steps a cell must undertake to replicate, a deeper
understanding of the structure and function of a cell’s genetic information is
necessary. A cell’s DNA, packaged as a double-stranded DNA molecule, is
called its genome. In prokaryotes, the genome is composed of a single,
double-stranded DNA molecule in the form of a loop or circle ({link]). The
region in the cell containing this genetic material is called a nucleoid. Some
prokaryotes also have smaller loops of DNA called plasmids that are not
essential for normal growth. Bacteria can exchange these plasmids with
other bacteria, sometimes receiving beneficial new genes that the recipient
can add to their chromosomal DNA. Antibiotic resistance is one trait that
often spreads through a bacterial colony through plasmid exchange.
Cell
membrane
Chromosomal DNA is
localized in a region
called the nucleoid.
Prokaryotes, including bacteria
and archaea, have a single,
circular chromosome located in a
central region called the nucleoid.
In eukaryotes, the genome consists of several double-stranded linear DNA
molecules ([link]). Each species of eukaryotes has a characteristic number
of chromosomes in the nuclei of its cells. Human body cells have 46
chromosomes, while human gametes (sperm or eggs) have 23
chromosomes each. A typical body cell, or somatic cell, contains two
matched sets of chromosomes, a configuration known as diploid. The letter
nis used to represent a single set of chromosomes; therefore, a diploid
organism is designated 2n. Human cells that contain one set of
chromosomes are called gametes, or sex cells; these are eggs and sperm,
and are designated 1n, or haploid.
There are 23 pairs of homologous
chromosomes in a female human
somatic cell. The condensed
chromosomes are viewed within
the nucleus (top), removed from a
cell in mitosis and spread out on a
Slide (right), and artificially
arranged according to length (left);
an arrangement like this is called a
karyotype. In this image, the
chromosomes were exposed to
fluorescent stains for
differentiation of the different
chromosomes. A method of
staining called “chromosome
painting” employs fluorescent
dyes that highlight chromosomes
in different colors. (credit:
National Human Genome
Project/NIH)
Matched pairs of chromosomes in a diploid organism are called
homologous (“same knowledge”) chromosomes. Homologous
chromosomes are the same length and have specific nucleotide segments
called genes in exactly the same location, or locus. Genes, the functional
units of chromosomes, determine specific characteristics by coding for
specific proteins. Traits are the variations of those characteristics. For
example, hair color is a characteristic with traits that are blonde, brown, or
black.
Each copy of a homologous pair of chromosomes originates from a
different parent; therefore, the genes themselves are not identical. The
variation of individuals within a species is due to the specific combination
of the genes inherited from both parents. Even a slightly altered sequence of
nucleotides within a gene can result in an alternative trait. For example,
there are three possible gene sequences on the human chromosome that
code for blood type: sequence A, sequence B, and sequence O. Because all
diploid human cells have two copies of the chromosome that determines
blood type, the blood type (the trait) is determined by which two versions of
the marker gene are inherited. It is possible to have two copies of the same
gene sequence on both homologous chromosomes, with one on each (for
example, AA, BB, or OO), or two different sequences, such as AB. These
different versions of genes are called alleles.
Minor variations of traits, such as blood type, eye color, and handedness,
contribute to the natural variation found within a species. However, if the
entire DNA sequence from any pair of human homologous chromosomes is
compared, the difference is less than one percent. The sex chromosomes, X
and Y, are the single exception to the rule of homologous chromosome
uniformity: Other than a small amount of homology that is necessary to
accurately produce gametes, the genes found on the X and Y chromosomes
are different.
Eukaryotic Chromosomal Structure and Compaction
If the DNA from all 46 chromosomes in a human cell nucleus was laid out
end to end, it would measure approximately two meters; however, its
diameter would be only 2 nm. Considering that the size of a typical human
cell is about 10 pm (100,000 cells lined up to equal one meter), DNA must
be tightly packaged to fit in the cell’s nucleus. At the same time, it must
also be readily accessible for the genes to be expressed. During some stages
of the cell cycle, the long strands of DNA are condensed into compact
chromosomes. There are a number of ways that chromosomes are
compacted.
In the first level of compaction, short stretches of the DNA double helix
wrap around a core of eight histone proteins at regular intervals along the
entire length of the chromosome ((link]). The DNA-histone complex is
called chromatin. The beadlike, histone DNA complex is called a
nucleosome, and DNA connecting the nucleosomes is called linker DNA. A
DNA molecule in this form is about seven times shorter than the double
helix without the histones, and the beads are about 10 nm in diameter, in
contrast with the 2-nm diameter of a DNA double helix. The next level of
compaction occurs as the nucleosomes and the linker DNA between them
are coiled into a 30-nm chromatin fiber. This coiling further shortens the
chromosome so that it is now about 50 times shorter than the extended
form. In the third level of packing, a variety of fibrous proteins is used to
pack the chromatin. These fibrous proteins also ensure that each
chromosome in a non-dividing cell occupies a particular area of the nucleus
that does not overlap with that of any other chromosome (see the top image
in [link)).
Organization of Eukaryotic Chromosomes
DNA double
helix
DNA wrapped
around histone
Nucleosomes
coiled into a
chromatin
fiber
Further
condensation
of chromatin
Duplicated
chromosome
Double-stranded DNA wraps
around histone proteins to form
nucleosomes that have the
appearance of “beads on a string.”
The nucleosomes are coiled into a
30-nm chromatin fiber. When a
cell undergoes mitosis, the
chromosomes condense even
further.
DNA replicates in the S phase of interphase. After replication, the
chromosomes are composed of two linked sister chromatids. When fully
compact, the pairs of identically packed chromosomes are bound to each
other by cohesin proteins. The connection between the sister chromatids is
closest in a region called the centromere. The conjoined sister chromatids,
with a diameter of about 1 jm, are visible under a light microscope. The
centromeric region is highly condensed and thus will appear as a constricted
area.
DNA Replication
By the end of this section, you will be able to:
e Explain the process of DNA replication
e Explain the importance of telomerase to DNA replication
e Describe mechanisms of DNA repair
When a cell divides, it is important that each daughter cell receives an
identical copy of the DNA. This is accomplished by the process of DNA
replication. The replication of DNA occurs during the synthesis phase, or S
phase, of the cell cycle, before the cell enters mitosis or meiosis.
The elucidation of the structure of the double helix provided a hint as to
how DNA is copied. Recall that adenine nucleotides pair with thymine
nucleotides, and cytosine with guanine. This means that the two strands are
complementary to each other. For example, a strand of DNA witha
nucleotide sequence of AGTCATGA will have a complementary strand
with the sequence TCAGTACT ((link]).
3!
LL LR) De
ee a ie ie a ee
ai
The two strands of DNA are
complementary, meaning the sequence of
bases in one strand can be used to create the
correct sequence of bases in the other strand.
Because of the complementarity of the two strands, having one strand
means that it is possible to recreate the other strand. This model for
replication suggests that the two strands of the double helix separate during
replication, and each strand serves as a template from which the new
complementary strand is copied ((Link]).
Semi-conservative model of DNA Replication
The semiconservative model of
DNA replication is shown. Gray
indicates the original DNA
strands, and blue indicates newly
synthesized DNA.
During DNA replication, each of the two strands that make up the double
helix serves as a template from which new strands are copied. The new
strand will be complementary to the parental or “old” strand. Each new
double strand consists of one parental strand and one new daughter strand.
This is known as semiconservative replication. When two DNA copies are
formed, they have an identical sequence of nucleotide bases and are divided
equally into two daughter cells.
DNA Replication in Eukaryotes
Because eukaryotic genomes are very complex, DNA replication is a very
complicated process that involves several enzymes and other proteins. It
occurs in three main stages: initiation, elongation, and termination.
Recall that eukaryotic DNA is bound to proteins known as histones to form
structures called nucleosomes. During initiation, the DNA is made
accessible to the proteins and enzymes involved in the replication process.
How does the replication machinery know where on the DNA double helix
to begin? It turns out that there are specific nucleotide sequences called
origins of replication at which replication begins. Certain proteins bind to
the origin of replication while an enzyme called helicase unwinds and
opens up the DNA helix. As the DNA opens up, Y-shaped structures called
replication forks are formed ((link]). Two replication forks are formed at
the origin of replication, and these get extended in both directions as
replication proceeds. There are multiple origins of replication on the
eukaryotic chromosome, such that replication can occur simultaneously
from several places in the genome.
During elongation, an enzyme called DNA polymerase adds DNA
nucleotides to the 3' end of the template. Because DNA polymerase can
only add new nucleotides at the end of a backbone, a primer sequence,
which provides this starting point, is added with complementary RNA
nucleotides. This primer is removed later, and the nucleotides are replaced
with DNA nucleotides. One strand, which is complementary to the parental
DNA strand, is synthesized continuously toward the replication fork so the
polymerase can add nucleotides in this direction. This continuously
synthesized strand is known as the leading strand. Because DNA
polymerase can only synthesize DNA ina 5' to 3' direction, the other new
strand is put together in short pieces called Okazaki fragments. The
Okazaki fragments each require a primer made of RNA to start the
synthesis. The strand with the Okazaki fragments is known as the lagging
strand. As synthesis proceeds, an enzyme removes the RNA primer, which
is then replaced with DNA nucleotides, and the gaps between fragments are
sealed by an enzyme called DNA ligase.
The process of DNA replication can be summarized as follows:
1. DNA unwinds at the origin of replication.
2. New bases are added to the complementary parental strands. One new
strand is made continuously, while the other strand is made in pieces.
3. Primers are removed, new DNA nucleotides are put in place of the
primers and the backbone is sealed by DNA ligase.
Helicase
<q”
3 XY 5' 3 5! 3] 5
Lagging
strand
RNA Okazaki Leading Newly made DNA
primer fragment strand DNA strands polymerase
A replication fork is formed by the opening of the
origin of replication, and helicase separates the
DNA strands. An RNA primer is synthesized, and
is elongated by the DNA polymerase. On the
leading strand, DNA is synthesized continuously,
whereas on the lagging strand, DNA is synthesized
in short stretches. The DNA fragments are joined
by DNA ligase (not shown).
Telomere Replication
Because eukaryotic chromosomes are linear, DNA replication comes to the
end of a line in eukaryotic chromosomes. As you have learned, the DNA
polymerase enzyme can add nucleotides in only one direction. In the
leading strand, synthesis continues until the end of the chromosome is
reached; however, on the lagging strand there is no place for a primer to be
made for the DNA fragment to be copied at the end of the chromosome.
This presents a problem for the cell because the ends remain unpaired, and
over time these ends get progressively shorter as cells continue to divide.
The ends of the linear chromosomes are known as telomeres, which have
repetitive sequences that do not code for a particular gene. As a
consequence, it is telomeres that are shortened with each round of DNA
replication instead of genes. For example, in humans, a six base-pair
sequence, TTAGGG, is repeated 100 to 1000 times. The discovery of the
enzyme telomerase ((link]) helped in the understanding of how
chromosome ends are maintained. The telomerase attaches to the end of the
chromosome, and complementary bases to the RNA template are added on
the end of the DNA strand. Once the lagging strand template is sufficiently
elongated, DNA polymerase can now add nucleotides that are
complementary to the ends of the chromosomes. Thus, the ends of the
chromosomes are replicated.
, ,
hg pW ea et a a a ft
CCATGCATTGGTTAG
GGTAC
9 decked 5’ CAAUCCCAAUC
telomerase
Telomerase has an associated RNA that complements
the 3’ overhang at the end of the chromosome.
SS a se ee
CCATGCATTGGTTAGGGTTAG
,GGTAC , GAAUGGCGAAUC
2 dendentenionts 5 telomerase
The RNA template is used to synthesize the complementary
strand. J
0 oe Co en
CCATGCATTGGTTAGGGTTAG
GET Ae. CAAUCCCAAUC
2! detentions 5 telomerase
Telomerase shifts, and the process is repeated.
}
, a
SS eS OO ee
CCATGCATTGGTTAGGGTTAGGGTTAG
GGTAC AATCCCAAT
3’ hedecledels 5’ 7 ee oe
Primase and DNA polymerase synthesize the complementary
strand.
The ends of linear chromosomes are
maintained by the action of the
telomerase enzyme.
Telomerase is typically found to be active in germ cells, adult stem cells,
and some cancer cells. For her discovery of telomerase and its action,
Elizabeth Blackburn ([link]) received the Nobel Prize for Medicine and
Physiology in 2009.
Elizabeth Blackburn, 2009 Nobel
Laureate, was the scientist who
discovered how telomerase works.
(credit: U.S. Embassy, Stockholm,
Sweden)
Telomerase is not active in adult somatic cells. Adult somatic cells that
undergo cell division continue to have their telomeres shortened. This
essentially means that telomere shortening is associated with aging. In
2010, scientists found that telomerase can reverse some age-related
conditions in mice, and this may have potential in regenerative medicine.
[footnote] Te]gmerase-deficient mice were used in these studies; these mice
have tissue atrophy, stem-cell depletion, organ system failure, and impaired
tissue injury responses. Telomerase reactivation in these mice caused
extension of telomeres, reduced DNA damage, reversed neurodegeneration,
and improved functioning of the testes, spleen, and intestines. Thus,
telomere reactivation may have potential for treating age-related diseases in
humans.
Mariella Jaskelioff, et al., “Telomerase reactivation reverses tissue
degeneration in aged telomerase-deficient mice,” Nature, 469 (2011):102-—7.
DNA Repair
DNA polymerase can make mistakes while adding nucleotides. It edits the
DNA by proofreading every newly added base. Incorrect bases are removed
and replaced by the correct base, and then polymerization continues
({link]a). Most mistakes are corrected during replication, although when
this does not happen, the mismatch repair mechanism is employed.
Mismatch repair enzymes recognize the wrongly incorporated base and
excise it from the DNA, replacing it with the correct base ({link]|b). In yet
another type of repair, nucleotide excision repair, the DNA double strand is
unwound and separated, the incorrect bases are removed along with a few
bases on the 5' and 3' end, and these are replaced by copying the template
with the help of DNA polymerase ((link]c). Nucleotide excision repair is
particularly important in correcting thymine dimers, which are primarily
caused by ultraviolet light. In a thymine dimer, two thymine nucleotides
adjacent to each other on one strand are covalently bonded to each other
rather than their complementary bases. If the dimer is not removed and
repaired it will lead to a mutation. Individuals with flaws in their nucleotide
excision repair genes show extreme sensitivity to sunlight and develop skin
cancers early in life.
3’
G
GGTTAGCCGATTCA
eekek lll A
lhl le aie lh lon
DNA polymerase
(a) Proofreading
(c) Nucleotide Excision
Proofreading by DNA polymerase
(a) corrects errors during
replication. In mismatch repair (b),
the incorrectly added base is
detected after replication. The
mismatch repair proteins detect
this base and remove it from the
newly synthesized strand by
nuclease action. The gap is now
filled with the correctly paired
base. Nucleotide excision (c)
repairs thymine dimers. When
exposed to UV, thymines lying
adjacent to each other can form
thymine dimers. In normal cells,
they are excised and replaced.
Most mistakes are corrected; if they are not, they may result in a mutation
—defined as a permanent change in the DNA sequence. Mutations in repair
genes may lead to serious consequences like cancer.
Prokaryotic Cell Division
Introduction
",..(T)he extreme rapidity with which generation succeeds generation
amongst bacteria offers to the forces of variation and natural selection a field
for their operation wholly unparalleled amongst higher forms of life."
Frederick W. Andrewes, "The Evolution of the Streptococci", The Lancet,
2:1415, 1906
Prokaryotes such as bacteria propagate by binary fission, and produces two
identical daughter cells. This is a simpler process than cell division in
eukaryotes, partly because there is no need for separate nuclear and cellular
divisions (mitosis and cytokinesis, respectively). As Andrewes noted, the
rapidity of cell reproduction in prokaryotes opens the door for rapid
evolutionary change in these organisms.
To achieve the outcome of identical daughter cells, some steps are essential.
The genomic DNA must be replicated and then allocated into the daughter
cells; the cytoplasmic contents must also be divided to give both new cells
the machinery to sustain life. In bacterial cells, the genome consists of a
single, circular DNA chromosome; therefore, the process of cell division is
simplified. Mitosis is unnecessary because there is no nucleus or multiple
chromosomes. This type of cell division is called binary fission.
Binary Fission
The cell division process of prokaryotes, called binary fission, is a less
complicated and much quicker process than cell division in eukaryotes.
Because of the speed of bacterial cell division, populations of bacteria can
grow very rapidly. The single, circular DNA chromosome of bacteria is not
enclosed in a nucleus, but instead occupies a specific location, the nucleoid,
within the cell. As in eukaryotes, the DNA of the nucleoid is associated with
proteins that aid in packaging the molecule into a compact size. The packing
proteins of bacteria are, however, related to some of the proteins involved in
the chromosome compaction of eukaryotes.
The starting point of replication, the origin, is close to the binding site of the
chromosome to the plasma membrane ([link]). Replication of the DNA is
bidirectional—moving away from the origin on both strands of the DNA
loop simultaneously. As the new double strands are formed, each origin point
moves away from the cell-wall attachment toward opposite ends of the cell.
As the cell elongates, the growing membrane aids in the transport of the
chromosomes. After the chromosomes have cleared the midpoint of the
elongated cell, cytoplasmic separation begins. A septum is formed between
the nucleoids from the periphery toward the center of the cell. When the new
cell walls are in place, the daughter cells separate.
Replication of the circular prokaryotic chromosome begins at the origin of replication
and continues in both directions at once.
Origin of replication
Prokaryotes have a single,
circular chromosome
FtsZ protein
The cell begins to elongate. FtsZ proteins migrate toward the midpoint of the cell.
The duplicated chromosomes separate and continue to move away from each other
toward opposite ends of the cell. FtsZ proteins form a ring around the periphery of the
midpoint between the chromosomes.
Cleavage furrow
FtsZ ring
The FtsZ ring directs the formation of a septum that divides the cell. Plasma membrane
and cell wall materials accumulate.
Septum
After the septum is complete, the cell pinches in two, forming two daughter cells. FtsZ is
dispersed throughout the cytoplasm of the new cells.
The binary fission of a bacterium is outlined in
five steps. (credit: modification of work by
“Mcstrother”/Wikimedia Commons)
Note:
Evolution in Action
Mitotic Spindle Apparatus
The precise timing and formation of the mitotic spindle is critical to the
success of eukaryotic cell division. Prokaryotic cells, on the other hand, do
not undergo mitosis and therefore have no need for a mitotic spindle.
However, the FtsZ protein that plays such a vital role in prokaryotic
cytokinesis is structurally and functionally very similar to tubulin, the
building block of the microtubules that make up the mitotic spindle fibers
that are necessary for eukaryotes. The formation of a ring composed of
repeating units of a protein called FtsZ directs the partition between the
nucleoids in prokaryotes. Formation of the FtsZ ring triggers the
accumulation of other proteins that work together to recruit new membrane
and cell-wall materials to the site. FtsZ proteins can form filaments, rings,
and other three-dimensional structures resembling the way tubulin forms
microtubules, centrioles, and various cytoskeleton components. In addition,
both FtsZ and tubulin employ the same energy source, GTP (guanosine
triphosphate), to rapidly assemble and disassemble complex structures.
FtsZ and tubulin are an example of homology, structures derived from the
same evolutionary origins. In this example, FtsZ is presumed to be similar
to the ancestor protein to both the modern FtsZ and tubulin. While both
proteins are found in extant organisms, tubulin function has evolved and
diversified tremendously since the evolution from its FtsZ-like prokaryotic
origin. A survey of cell-division machinery in present-day unicellular
eukaryotes reveals crucial intermediary steps to the complex mitotic
machinery of multicellular eukaryotes ([link]).
Mitotic Spindle Evolution
Structure of Division of
genetic nuclear Separation of
material material daughter cells
Mitotic Spindle Evolution
Prokaryotes
Some
protists
Structure of
genetic
material
There is no
nucleus. The
single,
circular
chromosome
exists ina
region of
cytoplasm
called the
nucleoid.
Linear
chromosomes
exist in the
nucleus.
Division of
nuclear
material
Occurs
through
binary fission.
As the
chromosome
is replicated,
the two copies
move to
opposite ends
of the cell by
an unknown
mechanism.
Chromosomes
attach to the
nuclear
envelope,
which
remains
intact. The
mitotic
spindle passes
through the
envelope and
elongates the
cell. No
centrioles
exist.
Separation of
daughter cells
FtsZ proteins
assemble into a
ring that
pinches the
cell in two.
Microfilaments
form a
cleavage
furrow that
pinches the
cell in two.
Mitotic Spindle Evolution
Structure of
genetic
material
Linear
chromosomes
exist in the
nucleus.
Other
protists
Division of
nuclear
material
Separation of
daughter cells
A mitotic
spindle forms
from the
centrioles and
passes
through the
nuclear
membrane,
which
remains
intact.
Chromosomes
attach to the
mitotic
spindle. The
mitotic
spindle
separates the
chromosomes
and elongates
the cell.
Microfilaments
form a
cleavage
furrow that
pinches the
cell in two.
Mitotic Spindle Evolution
Structure of
Division of
genetic nuclear Separation of
material material daughter cells
A mitotic
spindle forms
from the
centrioles.
The nuclear
envelope Microfilaments
Linear dissolves. form a
Animal chromosomes Chromosomes cleavage
cells exist in the attach to the furrow that
nucleus. mitotic pinches the
spindle, cell in two.
which
separates
them and
elongates the
cell.
The mitotic spindle fibers of eukaryotes are composed of microtubules.
Microtubules are polymers of the protein tubulin. The FtsZ protein active in
prokaryote cell division is very similar to tubulin in the structures it can form
and its energy source. Single-celled eukaryotes (such as yeast) display
possible intermediary steps between FtsZ activity during binary fission in
prokaryotes and the mitotic spindle in multicellular eukaryotes, during which
the nucleus breaks down and is reformed.
Eukaryotic Cell Cycle
Introduction
"These facts show that mitosis is due to the coordinate play of an extremely
complex system of forces which are as yet scarcely comprehended."
Edmund B. Wilson, The Cell in Development and Inheritance, pg. 86, 1896
Wilson was correct in regarding mitosis and cell division as being
"extremely complex". But in the century or so that has passed since he
wrote those words, we have learned quite a lot about the nature of that
complexity. The process has even been given a name: the cell cycle. The
cell cycle is an ordered series of events involving cell growth and cell
division that produces two new daughter cells. Cells on the path to cell
division proceed through a series of precisely timed and carefully regulated
stages of growth, DNA replication, and division that produce two
genetically identical cells. The cell cycle has two major phases: interphase
and the mitotic phase ([link]). During interphase, the cell grows and DNA
is replicated. During the mitotic phase, the replicated DNA and
cytoplasmic contents are separated and the cell divides.
Mitotic Phase
Interphase
Mitosis Formation
Cytokinesis ti caLginer
Ils
Interphase Interphase
A cell moves through a series of phases in an orderly
manner. During interphase, G, involves cell growth and
protein synthesis, the S phase involves DNA replication
and the replication of the centrosome, and G> involves
further growth and protein synthesis. The mitotic phase
follows interphase. Mitosis is nuclear division during
which duplicated chromosomes are segregated and
distributed into daughter nuclei. Usually the cell will
divide after mitosis in a process called cytokinesis in
which the cytoplasm is divided and two daughter cells
are formed.
Interphase
During interphase, the cell undergoes normal processes while also preparing
for cell division. For a cell to move from interphase to the mitotic phase,
many internal and external conditions must be met. The three stages of
interphase are called G,, S, and Gp.
G, Phase
The first stage of interphase is called the G, phase, or first gap, because
little change is visible under the microscope. However, during the G, stage,
the cell is quite active at the biochemical level. The cell is accumulating the
building blocks of chromosomal DNA and the associated proteins, as well
as accumulating enough energy reserves to complete the task of replicating
each chromosome in the nucleus.
S Phase
Throughout interphase, nuclear DNA remains in a semi-condensed
chromatin configuration. In the S phase (synthesis phase), DNA replication
results in the formation of two identical copies of each chromosome—sister
chromatids—that are firmly attached at the centromere region. At this stage,
each chromosome is made of two sister chromatids and is a duplicated
chromosome. The centrosome is duplicated during the S phase. The two
centrosomes will give rise to the mitotic spindle, the apparatus that
orchestrates the movement of chromosomes during mitosis. The centrosome
consists of a pair of rod-like centrioles at right angles to each other.
Centrioles help organize cell division. Centrioles are not present in the
centrosomes of many eukaryotic species, such as plants and most fungi.
G> Phase
In the Gp phase, or second gap, the cell replenishes its energy stores and
synthesizes the proteins necessary for chromosome manipulation. Some cell
organelles are duplicated, and the cytoskeleton is partially dismantled to
provide building blocks for the mitotic spindle. There may be additional
cell growth during G>. The final preparations for the mitotic phase must be
completed before the cell is able to enter the first stage of mitosis.
The Mitotic Phase
To make two daughter cells, the contents of the nucleus and the cytoplasm
must be divided. The mitotic phase is a multistep process during which the
duplicated chromosomes are aligned, separated, and moved to opposite
poles of the cell, and then the cell is divided into two new identical daughter
cells. The first portion of the mitotic phase, mitosis, is composed of five
stages, which accomplish nuclear division. The second portion of the
mitotic phase, called cytokinesis, is the physical separation of the
cytoplasmic components into two daughter cells.
Mitosis
Mitosis is divided into a series of phases—prophase, metaphase, anaphase,
and telophase—that result in the division of the cell nucleus (({Llink]).
* Chromosomes
condense and
become visible
* Spindle fibers
emerge from the
centrosomes
* Nuclear envelope
breaks down
+ Centrosomes
move toward
opposite poles
are lined up at
the metaphase
plate
Each sister
chromatid is
attached to a
spindle fiber
originating from
opposite poles
MITOSIS
« Centromeres
split in two
are pulled toward surrounds
opposite poles each set of
chromosomes
* Certain spindle
fibers begin to * The mitotic
elongate the cell spindle breaks
down
* Spindle fibers
continue to push
poles apart
cleavage furrow
separates the
daughter cells
* Plant cells: a cell
precursor toa
new cell wall,
separates the
daughter cells
Animal cell mitosis is divided into four stages—prophase, metaphase,
anaphase, and telophase—visualized here by light microscopy with
fluorescence. Mitosis is usually accompanied by cytokinesis, shown
here by a transmission electron microscope. (credit "diagrams":
modification of work by Mariana Ruiz Villareal; credit "mitosis
micrographs": modification of work by Roy van Heesbeen; credit
"cytokinesis micrograph": modification of work by the Wadsworth
Center, NY State Department of Health; donated to the Wikimedia
foundation; scale-bar data from Matt Russell)
During prophase, the “first phase,” several events must occur to provide
access to the chromosomes in the nucleus. The nuclear envelope starts to
break into small vesicles, and the Golgi apparatus and endoplasmic
reticulum fragment and disperse to the periphery of the cell. The nucleolus
disappears. The centrosomes begin to move to opposite poles of the cell.
The microtubules that form the basis of the mitotic spindle extend between
the centrosomes, pushing them farther apart as the microtubule fibers
lengthen. The sister chromatids begin to coil more tightly and become
visible under a light microscope. Also, each sister chromatid attaches to
spindle microtubules at the centromere via a protein complex called the
kinetochore.
During metaphase, all of the chromosomes are aligned in a plane called the
metaphase plate, or the equatorial plane, midway between the two poles of
the cell. The sister chromatids are still tightly attached to each other. At this
time, the chromosomes are maximally condensed.
During anaphase, the sister chromatids at the equatorial plane are split
apart at the centromere. Each chromatid, now called a chromosome, is
pulled rapidly toward the centrosome to which its microtubule was
attached. The cell becomes visibly elongated as the non-kinetochore
microtubules slide against each other at the metaphase plate where they
overlap.
During telophase, all of the events that set up the duplicated chromosomes
for mitosis during the first three phases are reversed. The chromosomes
reach the opposite poles and begin to decondense (unravel). The mitotic
spindles are broken down into monomers that will be used to assemble
cytoskeleton components for each daughter cell. Nuclear envelopes form
around chromosomes.
Cytokinesis
Cytokinesis is the second part of the mitotic phase during which cell
division is completed by the physical separation of the cytoplasmic
components into two daughter cells. Although the stages of mitosis are
similar for most eukaryotes, the process of cytokinesis is quite different for
eukaryotes that have cell walls, such as plant cells.
In cells such as animal cells that lack cell walls, cytokinesis begins
following the onset of anaphase. A contractile ring composed of actin
filaments forms just inside the plasma membrane at the former metaphase
plate. The actin filaments pull the equator of the cell inward, forming a
fissure. This fissure, or “crack,” is called the cleavage furrow. The furrow
deepens as the actin ring contracts, and eventually the membrane and cell
are cleaved in two ([link]).
In plant cells, a cleavage furrow is not possible because of the rigid cell
walls surrounding the plasma membrane. A new cell wall must form
between the daughter cells. During interphase, the Golgi apparatus
accumulates enzymes, structural proteins, and glucose molecules prior to
breaking up into vesicles and dispersing throughout the dividing cell.
During telophase, these Golgi vesicles move on microtubules to collect at
the metaphase plate. There, the vesicles fuse from the center toward the cell
walls; this structure is called a cell plate. As more vesicles fuse, the cell
plate enlarges until it merges with the cell wall at the periphery of the cell.
Enzymes use the glucose that has accumulated between the membrane
layers to build a new cell wall of cellulose. The Golgi membranes become
the plasma membrane on either side of the new cell wall ({link]).
(a) Animal cell
Cleavage
furrow E>
Contractile
ring
Cell
8 ~
Golgi vesicles
(b) Plant cell
In part (a), a cleavage furrow forms at
the former metaphase plate in the
animal cell. The plasma membrane is
drawn in by a ring of actin fibers
contracting just inside the membrane.
The cleavage furrow deepens until the
cells are pinched in two. In part (b),
Golgi vesicles coalesce at the former
metaphase plate in a plant cell. The
vesicles fuse and form the cell plate.
The cell plate grows from the center
toward the cell walls. New cell walls
are made from the vesicle contents.
G, Phase
Not all cells adhere to the classic cell-cycle pattern in which a newly
formed daughter cell immediately enters interphase, closely followed by the
mitotic phase. Cells in the Gp phase are not actively preparing to divide.
The cell is in a quiescent (inactive) stage, having exited the cell cycle. Some
cells enter Gg temporarily until an external signal triggers the onset of G,.
Other cells that never or rarely divide, such as mature cardiac muscle and
nerve cells, remain in Gp permanently ((link]).
Gy
Cells not
actively
dividing
Cell Cycle
Cells that are not actively
preparing to divide enter an
alternate phase called Go. In some
cases, this is a temporary
condition until triggered to enter
G,. In other cases, the cell will
remain in Gp permanently.
Control of the Cell Cycle
The length of the cell cycle is highly variable even within the cells of an
individual organism. In humans, the frequency of cell turnover ranges from
a few hours in early embryonic development to an average of two to five
days for epithelial cells, or to an entire human lifetime spent in Gp by
specialized cells such as cortical neurons or cardiac muscle cells. There is
also variation in the time that a cell spends in each phase of the cell cycle.
When fast-dividing mammalian cells are grown in culture (outside the body
under optimal growing conditions), the length of the cycle is approximately
24 hours. In rapidly dividing human cells with a 24-hour cell cycle, the G;
phase lasts approximately 11 hours. The timing of events in the cell cycle is
controlled by mechanisms that are both internal and external to the cell.
Regulation at Internal Checkpoints
It is essential that daughter cells be exact duplicates of the parent cell.
Mistakes in the duplication or distribution of the chromosomes lead to
mutations that may be passed forward to every new cell produced from the
abnormal cell. To prevent a compromised cell from continuing to divide,
there are internal control mechanisms that operate at three main cell cycle
checkpoints at which the cell cycle can be stopped until conditions are
favorable. These checkpoints occur near the end of Gj, at the G>-M
transition, and during metaphase ((link]).
Mitotic Phase
G, Checkpoint
M Checkpoint Formation
of 2 daughter
cells
G, Checkpoint
(restriction)
The cell cycle is controlled at three checkpoints.
Integrity of the DNA is assessed at the G;
checkpoint. Proper chromosome duplication is
assessed at the G» checkpoint. Attachment of each
kinetochore to a spindle fiber is assessed at the M
checkpoint.
The G, Checkpoint
The G, checkpoint determines whether all conditions are favorable for cell
division to proceed. The G, checkpoint, also called the restriction point, is
the point at which the cell irreversibly commits to the cell-division process.
In addition to adequate reserves and cell size, there is a check for damage to
the genomic DNA at the G, checkpoint. A cell that does not meet all the
requirements will not be released into the S phase.
The Gy Checkpoint
The G> checkpoint bars the entry to the mitotic phase if certain conditions
are not met. As in the G, checkpoint, cell size and protein reserves are
assessed. However, the most important role of the G» checkpoint is to
ensure that all of the chromosomes have been replicated and that the
replicated DNA is not damaged.
The M Checkpoint
The M checkpoint occurs near the end of the metaphase stage of mitosis.
The M checkpoint is also known as the spindle checkpoint because it
determines if all the sister chromatids are correctly attached to the spindle
microtubules. Because the separation of the sister chromatids during
anaphase is an irreversible step, the cycle will not proceed until the
kinetochores of each pair of sister chromatids are firmly anchored to spindle
fibers arising from opposite poles of the cell.
Cancer and the Cell Cycle
Introduction
" While there are several chronic diseases more destructive to life than
cancer, none is more feared." Charles Mayo, 1926
Mayo's words are still true today; a diagnosis of cancer is a fearful thing.
But what is cancer? Cancer is a collective name for many different
diseases caused by a common mechanism: uncontrolled cell division.
Despite the redundancy and overlapping levels of control of cell division,
errors occur. One of the critical processes monitored by the cell-cycle
checkpoint surveillance mechanism is the proper replication of DNA during
the S phase. Even when all of the cell-cycle controls are fully functional, a
small percentage of replication errors (mutations) will be passed on to the
daughter cells. If one of these changes to the DNA nucleotide sequence
occurs within a gene, a gene mutation results. All cancers begin when a
gene mutation gives rise to a faulty protein that participates in the process
of cell reproduction. The change in the cell that results from the malformed
protein may be minor. Even minor mistakes, however, may allow
subsequent mistakes to occur more readily. Over and over, small,
uncorrected errors are passed from parent cell to daughter cells and
accumulate as each generation of cells produces more non-functional
proteins from uncorrected DNA damage. Eventually, the pace of the cell
cycle speeds up as the effectiveness of the control and repair mechanisms
decreases. Uncontrolled growth of the mutated cells outpaces the growth of
normal cells in the area, and a cancerous tumor can result.
Some definitions
All of us have heard the words cancer, tumor, malignancy, metastasis, etc.
But it is important to understand the definitions of these words, and others,
before we get into a discussion of the causes of the disease we know as
cancer. In previous sections you learned about the cell cycle, which controls
mitosis, and thus controls the growth of cells, tissues, and organs. If there is
a malfunction at one of the checkpoints of the cell cycle, leading to mitosis
in cells that would otherwise not divide, it would result in a population of
cells which have lost control over how and when they divide. This
accumulation of cells is called a neoplasm (from the Greek veo- neo- "new"
and mAdopa plasma "formation, creation"). A neoplasm that forms a visible
or palpable lump in the body is called a tumor. Tumors can be benign, or
malignant, depending on how fast they grow and how readily (or not) they
spread to other tissues. An example of a benign tumor would be a wart.
These usually grow slowly and the cells, although they have lost cell-cycle
control, do not spread to adjacent or distant tissues. A malignant neoplasm
is what most people would call cancer; it grows more rapidly and can
spread to adjacent or even distant sites in the body (a process known as
metastasis. The number of blood vessels providing nutrients to the tumor
may also increase (a process known as tumor angiogenesis).
Characteristics of cancer cells
What are the characteristics of a cancer cell, and how does it differ from a
normal cell? Over the decades scientists have discovered many
morphological and physiological differences ([link]), and studying those
differences led to many of the advances in our knowledge of the cell cycle
and its regulation. Cancer biologists have summarized and analyzed many
of these known differences. It is known that cancer can result from
mutations in many genes, and that cancers in different organs differ in their
physiology, appearance, growth rate, and many other parameters. But when
they filtered through all the data, they concluded that there are six essential
alterations in cell physiology that are important hallmarks of the malignant
state.
Cancer and normal cells
Normal and Cancer Cells
under the microscope
Large, variably shaped nuclei
Many dividing cells;
Y
x P isd
<= ~~... | Disorganized arrangement
fone
ee re
ae 4
ie SS
Variation in size and shape
Loss of normal features
Some characteristics of cancer cells, compared to normal cells. Figure
courtesy of Dr. Wayne LaMorte, Boston University School of Public
Health.
e Self-sufficiency in growth signals (positive cell-cycle regulators):
Cancer cells have an unregulated ability to proliferate. This
uncontrolled mitosis often occurs via the activation of oncogenes
(literally, a gene that can cause cancer). Many of these genes code for
enzymes, such as the protein kinase known as Cdk (see below) or Src,
which become hyperactive when mutated; this hyperactivity drives
unregulated cell proliferation (see below).
e Insensitivity to growth-inhibitory signals (negative cell cycle
regulators): Cancer cells inactivate so-called tumor suppressor genes,
such as RB1 or p53 (see below), that normally act at certain points in
the cell cycle to inhibit mitosis (see below).
e Evasion of programmed cell death (apoptosis): cancer cells suppress
and inactivate genes and pathways that normally cause cells to die.
e Unlimited replication potential: Cancer cells activate specific gene
pathways that render them immortal even after generations of growth.
HeLa cells, a human cancer cell derived from a cervical carcinoma in
the 1950's, are busily proliferating in labs around the world today, long
after the cancer victim passed away.
e Sustained angiogenesis (ability to make new blood vessels and obtain
nutrients via increased blood flow): Many cancer cells acquire the
capacity to induce growth of blood vessels into the tumor; this is
known as tumor angiogenesis.
e Tissue invasion and metastasis: Most normal cells do not migrate, nor
do they invade surrounding tissues; cancer cells acquire the capacity to
migrate to other organs, invade other tissues, and colonize these
organs, resulting in their spread throughout the body. This process is
called metastasis.
Proto-oncogenes
The genes that code for the positive cell-cycle regulators are called proto-
oncogenes. Proto-oncogenes are normal genes that, when mutated, become
oncogenes—¢genes that cause a cell to become cancerous. Consider what
might happen to the cell cycle in a cell with a recently acquired oncogene.
In most instances, the alteration of the DNA sequence will result in a less
functional (or non-functional) protein. The result is detrimental to the cell
and will likely prevent the cell from completing the cell cycle; however, the
organism is not harmed because the mutation will not be carried forward. If
a cell cannot reproduce, the mutation is not propagated and the damage is
minimal. Occasionally, however, a gene mutation causes a change that
increases the activity of a positive regulator. For example, a mutation that
allows Cdk, a protein involved in cell-cycle regulation, to be activated
before it should be could push the cell cycle past a checkpoint before all of
the required conditions are met. If the resulting daughter cells are too
damaged to undertake further cell divisions, the mutation would not be
propagated and no harm comes to the organism. However, if the atypical
daughter cells are able to divide further, the subsequent generation of cells
will likely accumulate even more mutations, some possibly in additional
genes that regulate the cell cycle.
The Cdk example is only one of many genes that are considered proto-
oncogenes. In addition to the cell-cycle regulatory proteins, any protein that
influences the cycle can be altered in such a way as to override cell-cycle
checkpoints. Once a proto-oncogene has been altered such that there is an
increase in the rate of the cell cycle, it is then called an oncogene.
Tumor Suppressor Genes
Like proto-oncogenes, many of the negative cell-cycle regulatory proteins
were discovered in cells that had become cancerous. Tumor suppressor
genes are genes that code for the negative regulator proteins, the type of
regulator that—when activated—can prevent the cell from undergoing
uncontrolled division. The collective function of the best-understood tumor
suppressor gene proteins, retinoblastoma protein (RB1), p53, and p21, is to
put up a roadblock to cell-cycle progress until certain events are completed.
A cell that carries a mutated form of a negative regulator might not be able
to halt the cell cycle if there is a problem.
Mutated p53 genes have been identified in more than half of all human
tumor cells. This discovery is not surprising in light of the multiple roles
that the p53 protein plays at the G, checkpoint. The p53 protein activates
other genes whose products halt the cell cycle (allowing time for DNA
repair), activates genes whose products participate in DNA repair, or
activates genes that initiate cell death when DNA damage cannot be
repaired. A damaged p53 gene can result in the cell behaving as if there are
no mutations ([link]). This allows cells to divide, propagating the mutation
in daughter cells and allowing the accumulation of new mutations. In
addition, the damaged version of p53 found in cancer cells cannot trigger
cell death.
= Cells can become cancerous
When cellular damage occurs. p53 arrests Mutated p53 does not arrest the cell cycle.
the cell cycle until the damage is repaired. The damaged cell continues to divide,
If damage cannot be repaired, apoptosis which may result in cancer.
occurs.
(a) The role of p53 is to monitor DNA. If damage is
detected, p53 triggers repair mechanisms. If repairs are
unsuccessful, p53 signals apoptosis. (b) A cell with an
abnormal p53 protein cannot repair damaged DNA and
cannot signal apoptosis. Cells with abnormal p53 can
become cancerous. (credit: modification of work by
Thierry Soussi)
Transcription
Introduction
"My own thinking (and that of many of my colleagues) is based on two
general principles, which I shall call the Sequence Hypothesis and the
Central Dogma. The direct evidence for both of them is negligible, but I
have found them to be of great help in getting to grips with these very
complex problems. I present them here in the hope that others can make
similar use of them. Their speculative nature is emphasized by their names.
It is an instructive exercise to attempt to build a useful theory without using
them. One generally ends in the wilderness. The Sequence Hypothesis
This has already been referred to a number of times. In its simplest form it
assumes that the specificity of a piece of nucleic acid is expressed solely by
the sequence of its bases, and that this sequence is a (simple) code for the
amino acid sequence of a particular protein... The Central Dogma This
states that once ‘information’ has passed into protein it cannot get out again.
In more detail, the transfer of information from nucleic acid to nucleic acid,
or from nucleic acid to protein may be possible, but transfer from protein to
protein, or from protein to nucleic acid is impossible. Information means
here the precise determination of sequence, either of bases in the nucleic
acid or of amino acid residues in the protein. This is by no means
universally held—Sir Macfarlane Burnet, for example, does not subscribe
to it—but many workers now think along these lines. As far as I know it has
not been explicitly stated before. " Francis Crick, 1958
Crick's concept of the Central Dogma of Molecular Biology is a useful way
to summarize a lot of what we know about nucleic acids. In both
prokaryotes and eukaryotes, the second function of DNA (the first was
replication) is to provide the information needed to construct the proteins
necessary so that the cell can perform all of its functions. To do this, the
DNA is “read” or transcribed into an mRNA molecule. The mRNA then
provides the code to form a protein by a process called translation. Through
the processes of transcription and translation, a protein is built with a
specific sequence of amino acids that was originally encoded in the DNA.
This section discusses the details of transcription.
The Central Dogma of Molecular Biology: DNA Encodes RNA;
RNA Encodes Protein
The flow of genetic information in cells from DNA to mRNA to protein is
described by the Central Dogma of Molecular Biology ((link]), which
States that genes specify the sequences of mRNAs, which in turn specify the
sequences of proteins.
Protein
The central dogma of molecular
biology states that DNA encodes
RNA, which in turn encodes
protein.
The copying of DNA to mRNA is relatively straightforward, with one
nucleotide being added to the mRNA strand for every complementary
nucleotide read in the DNA strand. The translation to protein is more
complex because groups of three mRNA nucleotides correspond to one
amino acid of the protein sequence. However, as we shall see in the next
section, the translation to protein is still systematic, such that nucleotides 1
to 3 correspond to amino acid 1, nucleotides 4 to 6 correspond to amino
acid 2, and so on.
Transcription: from DNA to mRNA
Both prokaryotes and eukaryotes perform fundamentally the same process
of transcription, with the important difference of the membrane-bound
nucleus in eukaryotes. With the genes bound in the nucleus, transcription
occurs in the nucleus of the cell and the mRNA transcript must be
transported to the cytoplasm. The prokaryotes, which include bacteria and
archaea, lack membrane-bound nuclei and other organelles, and
transcription occurs in the cytoplasm of the cell. In both prokaryotes and
eukaryotes, transcription occurs in three main stages: initiation, elongation,
and termination.
Initiation
Transcription requires the DNA double helix to partially unwind in the
region of mRNA synthesis. The region of unwinding is called a
transcription bubble. The DNA sequence onto which the proteins and
enzymes involved in transcription bind to initiate the process is called a
promoter. In most cases, promoters exist upstream of the genes they
regulate. The specific sequence of a promoter is very important because it
determines whether the corresponding gene is transcribed all of the time,
some of the time, or hardly at all ([link]).
DNA RNA
nontemplate
strand
RNA polymerase
DNA
template
strand Promoter
The initiation of transcription begins
when DNA is unwound, forming a
transcription bubble. Enzymes and
other proteins involved in
transcription bind at the promoter.
Elongation
Transcription always proceeds from one of the two DNA strands, which is
called the template strand. The mRNA product is complementary to the
template strand and is almost identical to the other DNA strand, called the
nontemplate strand, with the exception that RNA contains a uracil (U) in
place of the thymine (T) found in DNA. During elongation, an enzyme
called RNA polymerase proceeds along the DNA template adding
nucleotides by base pairing with the DNA template in a manner similar to
DNA replication, with the difference that an RNA strand is being
synthesized that does not remain bound to the DNA template. As elongation
proceeds, the DNA is continuously unwound ahead of the core enzyme and
rewound behind it ([link]).
Nontemplate strand
G
CcGCACTC
ATGCCGCA 4
Dj . “4
““Ection of Be ea 3
©
v GATSSTSCAT
5 3’
TACCACGTA
CS
UY
TASSSSS7 1 CACC Che CAUS
3
TGeotcaGtaS
5!
DNA RNA polymerase Template strand
During elongation, RNA polymerase tracks along the
DNA template, synthesizes mRNA in the 5' to 3'
direction, and unwinds then rewinds the DNA as it is
read.
Termination
Once a gene is transcribed, the prokaryotic polymerase needs to be
instructed to dissociate from the DNA template and liberate the newly made
mRNA. Depending on the gene being transcribed, there are two kinds of
termination signals, but both involve repeated nucleotide sequences in the
DNA template that result in RNA polymerase stalling, leaving the DNA
template, and freeing the mRNA transcript.
On termination, the process of transcription is complete. In a prokaryotic
cell, by the time termination occurs, the transcript would already have been
used to partially synthesize numerous copies of the encoded protein because
these processes can occur concurrently using multiple ribosomes
(polyribosomes) ([link]). In contrast, the presence of a nucleus in eukaryotic
cells precludes simultaneous transcription and translation.
+ Polyribosome
Multiple polymerases can transcribe a single
bacterial gene while numerous ribosomes
concurrently translate the mRNA transcripts
into polypeptides. In this way, a specific
protein can rapidly reach a high
concentration in the bacterial cell.
Eukaryotic RNA Processing
The newly transcribed eukaryotic mRNAs must undergo several processing
steps before they can be transferred from the nucleus to the cytoplasm and
translated into a protein. The additional steps involved in eukaryotic MRNA
maturation create a molecule that is much more stable than a prokaryotic
mRNA. For example, eukaryotic mRNAs last for several hours, whereas the
typical prokaryotic mRNA lasts no more than five seconds.
The mRNA transcript is first coated in RNA-stabilizing proteins to prevent
it from degrading while it is processed and exported out of the nucleus. This
occurs while the pre-mRNA still is being synthesized by adding a special
nucleotide “cap” to the 5' end of the growing transcript. In addition to
preventing degradation, factors involved in protein synthesis recognize the
cap to help initiate translation by ribosomes.
Once elongation is complete, an enzyme then adds a string of
approximately 200 adenine residues to the 3' end, called the poly-A tail.
This modification further protects the pre-mRNA from degradation and
signals to cellular factors that the transcript needs to be exported to the
cytoplasm.
Eukaryotic genes are composed of protein-coding sequences called exons
(ex-on signifies that they are expressed) and intervening sequences called
introns (int-ron denotes their intervening role). Introns are removed from
the pre-mRNA during processing. Intron sequences in MRNA do not
encode functional proteins. It is essential that all of a pre-mRNA’s introns
be completely and precisely removed before protein synthesis so that the
exons join together to code for the correct amino acids. If the process errs
by even a single nucleotide, the sequence of the rejoined exons would be
shifted, and the resulting protein would be nonfunctional. The process of
removing introns and reconnecting exons is called splicing ({link]). Introns
are removed and degraded while the pre-mRNA is still in the nucleus.
Primary RNA transcript
l RNA processing
Spliced RNA
5' cap Poly-A tail
5’ untranslated 3’ untranslated
region region
Eukaryotic MRNA contains introns that
must be spliced out. A 5' cap and 3' tail
are also added.
Translation
Introduction
" Protein synthesis is a central problem for the whole of biology, and that it
is in all probability closely related to gene action. " Francis Crick, 1958
Crick's words are still true today. The synthesis of proteins is one of a cell’s
most complicated and energy-consuming metabolic processes, and the
evolution of this complex process remains one of the hardest questions to
answer. But the products of protein synthesis (proteins) indeed are closely
related to gene action. In addition, proteins account for more mass than any
other component of living organisms (with the exception of water), and
proteins perform a wide variety of the functions of a cell. The process of
translation, or protein synthesis, involves decoding an mRNA message into
a polypeptide product, in which amino acids are covalently strung together
in lengths ranging from approximately 50 amino acids to more than 1,000.
The Protein Synthesis Machinery
In addition to the mRNA template, many other molecules contribute to the
process of translation. The composition of each component may vary across
species; for instance, ribosomes may consist of different numbers of
ribosomal RNAs (rRNA) and polypeptides depending on the organism.
However, the general structures and functions of the protein synthesis
machinery are comparable from bacteria to human cells. Translation
requires the input of an mRNA template, ribosomes, tRNAs, and various
enzymatic factors ([link]).
Amino acids
Growing
protein chain Ribosome
tRNA
mRNA
The protein synthesis machinery
includes the large and small
subunits of the ribosome, mRNA,
and tRNA. (credit: modification of
work by NIGMS, NIH)
In E. coli, there are 200,000 ribosomes present in every cell at any given
time. A ribosome is a complex macromolecule composed of structural and
catalytic rRNAs, and many distinct polypeptides. In eukaryotes, the
nucleolus is completely specialized for the synthesis and assembly of
rRNAs.
Ribosomes are located in the cytoplasm and on the plasma membrane of
prokaryotes, and in the cytoplasm and endoplasmic reticulum of eukaryotes.
Ribosomes are made up of a large and a small subunit that come together
for translation. The small subunit is responsible for binding the mRNA
template, whereas the large subunit sequentially binds tRNAs, a type of
RNA molecule that brings amino acids to the growing chain of the
polypeptide. Each mRNA molecule is simultaneously translated by many
ribosomes, all synthesizing protein in the same direction.
Depending on the species, 40 to 60 types of tRNA exist in the cytoplasm.
Serving as adaptors, specific tRNAs bind to sequences on the mRNA
template and add the corresponding amino acid to the polypeptide chain.
Therefore, tRNAs are the molecules that actually “translate” the language
of RNA into the language of proteins. For each tRNA to function, it must
have its specific amino acid bonded to it. In the process of tRNA
“charging,” each tRNA molecule is bonded to its correct amino acid.
The Genetic Code
To summarize what we know to this point, the cellular process of
transcription generates messenger RNA (MRNA), a mobile molecular copy
of one or more genes with an alphabet of A, C, G, and uracil (U).
Translation of the mRNA template converts nucleotide-based genetic
information into a protein product. Protein sequences consist of 20
commonly occurring amino acids; therefore, it can be said that the protein
alphabet consists of 20 letters. Each amino acid is defined by a three-
nucleotide sequence called the triplet codon. The relationship between a
nucleotide codon and its corresponding amino acid is called the genetic
code.
Given the different numbers of “letters” in the mRNA and protein
“alphabets,” combinations of nucleotides corresponded to single amino
acids. Using a three-nucleotide code means that there are a total of 64 (4 x 4
x 4) possible combinations; therefore, a given amino acid is encoded by
more than one nucleotide triplet ({link]).
Second letter
First letter
Third letter
This figure shows the genetic code for translating
each nucleotide triplet, or codon, in MRNA into an
amino acid or a termination signal in a nascent
protein. (credit: modification of work by NIH)
Three of the 64 codons terminate protein synthesis and release the
polypeptide from the translation machinery. These triplets are called stop
codons. Another codon, AUG, also has a special function. In addition to
specifying the amino acid methionine, it also serves as the start codon to
initiate translation. The reading frame for translation is set by the AUG start
codon near the 5' end of the mRNA. The genetic code is universal. With a
few exceptions, virtually all species use the same genetic code for protein
synthesis, which is powerful evidence that all life on Earth shares a
common origin.
The Mechanism of Protein Synthesis
Just as with mRNA synthesis, protein synthesis can be divided into three
phases: initiation, elongation, and termination. The process of translation is
similar in prokaryotes and eukaryotes. Here we will explore how translation
occurs in E. coli, a representative prokaryote, and specify any differences
between prokaryotic and eukaryotic translation.
Protein synthesis begins with the formation of an initiation complex. In E.
coli, this complex involves the small ribosome subunit, the mRNA
template, three initiation factors, and a special initiator tRNA. The initiator
tRNA interacts with the AUG start codon, and links to a special form of the
amino acid methionine that is typically removed from the polypeptide after
translation is complete.
In prokaryotes and eukaryotes, the basics of polypeptide elongation are the
same, so we will review elongation from the perspective of E. coli. The
large ribosomal subunit of E. coli consists of three compartments: the A site
binds incoming charged tRNAs (tRNAs with their attached specific amino
acids). The P site binds charged tRNAs carrying amino acids that have
formed bonds with the growing polypeptide chain but have not yet
dissociated from their corresponding tRNA. The E site releases dissociated
tRNAs so they can be recharged with free amino acids. The ribosome shifts
one codon at a time, catalyzing each process that occurs in the three sites.
With each step, a charged tRNA enters the complex, the polypeptide
becomes one amino acid longer, and an uncharged tRNA departs. The
energy for each bond between amino acids is derived from GTP, a molecule
similar to ATP ([link]). Amazingly, the E. coli translation apparatus takes
only 0.05 seconds to add each amino acid, meaning that a 200-amino acid
polypeptide could be translated in just 10 seconds.
Ribosome large
subunit
Small Ribosomal
subunit
Polypeptide chain
Translation begins when a tRNA
anticodon recognizes a codon on
the mRNA. The large ribosomal
subunit joins the small subunit,
and a second tRNA is recruited.
As the mRNA moves relative to
the ribosome, the polypeptide
chain is formed. Entry of a release
factor into the A site terminates
translation and the components
dissociate.
Termination of translation occurs when a stop codon (UAA, UAG, or UGA)
is encountered. When the ribosome encounters the stop codon, the growing
polypeptide is released and the ribosome subunits dissociate and leave the
mRNA. After many ribosomes have completed translation, the mRNA is
degraded so the nucleotides can be reused in another transcription reaction.
Connection Between DNA and Phenotype
You CAN get there from here...
In the beginning was the word
WORD
WORE
GORE
GONE
GENE
and by the mutation came the gene.
Michael A. Arbib, Towards a Theoretical Biology: An IUBS Symposium,
1969
Sickle Cell Anemia: A look at the connection between DNA and
Phenotype
Changes in the DNA sequence of a gene are known as mutations. Because
genes code for and are translated into proteins, mutations often (but not
always) result in changes in the sequence of amino acids in those proteins.
Changes in the amino acid sequence can modify or even completely destroy
protein function. Proteins have many functions within cells, and a change in
those functions results in a change in the phenotype of that cell or organism.
So a mutation as simple as a single base change in a DNA sequence can
have dramatic effects on phenotype. One of the best examples of this
phenomenon can be observed when mutations occur in the gene for one of
the protein components of the red blood cell protein we call hemoglobin.
A major component of the erythrocytes (red blood cells) found in ver-
tebrates is hemoglobin. A molecule of hemoglobin from a normal adult
human contains 4 proteins (two identical alpha polypeptides and two
identical beta polypeptides) surrounding a core of heme (contains complex
molecule containing an atom of iron which can combine reversibly with
oxygen). Thus, hemoglobin functions as the major oxygen-carrying
constituent of blood. Because of hemoglobin, a given volume of blood can
carry far more oxygen than could be dissolved in an equal volume of water.
The polypeptides that make up the hemoglobin are produced by the
processes of transcription and translation. So, the instructions for making
the polypeptides are stored in the DNA, and the specific region on the DNA
that codes for the polypeptide is called a gene. The physical location of the
gene on the chromosome is the locus. If you remember from the earlier
section on protein structure and function, the sequence of amino acids in a
polypeptide can have a significant effect on the overall function of the
protein. Since the sequence of nucleotides in the DNA codes for a particular
sequence of amino acids in the polypeptide, it is logical to conclude that
changes in the nucleotide sequence in the DNA can change the sequence of
amino acids in the polypeptide and thereby changing how the polypeptide
functions.
In many human populations, particularly those with origins in Central
Africa or the Mediterranean, there are individuals who suffer from severe
anemia and whose blood contains numerous distorted, sickle-shaped
erythrocytes ([link]). Hence, the disease was given the name sickle-cell
anemia.
Notice the sickle shaped cells in the image. By
Dr Graham Beards via Wikimedia Commons
Sickle-cell anemia is one of the most studied and well-understood genetic
diseases. In spite of this level of understanding, there is currently no
effective treatment for the disease. Experimental bone marrow transplants
have cured the disease in some patients, but bone marrow transplants are
currently recommended in only a handful of cases. In the United States
alone, there are 50,000 individuals with sickle-cell anemia.
Biochemical studies established that the gene affected in sickle-cell anemia
has the code for an abnormal beta polypeptide, which is one of the
components of the hemoglobin molecule. Therefore, there are two different
forms of the hemoglobin gene that codes for the beta chain:
Form 1: Hb“ has the code for a normal beta chain
Form 2: Hb has the code for an abnormal beta chain
Hb“ and HbS are considered alleles. The word “allele” comes from the
same root as “alternative.” Thus, alleles are alternative forms of the same
gene. Alleles arise by mutation. Mutations come about by many different
ways, but what is common among the different types of mutations is a
change in the order of nucleotides in the DNA. Thinking back to the Central
Dogma of Molecular Biology, one can reword it with the above in mind.
Changes in the DNA causes changes in RNA which can cause changes in
the polypeptide and a new polypeptide is a new phenotype.
Humans are diploid organisms; they have two copies of most genes.
However, the two copies they possess do not have to be identical. When
there are two possible alleles for a gene (such as in the gene for the beta
chain of hemoglobin), a diploid individual will have one of three possible
combinations of the two alleles. They can be Hb“ Hb“ , Hb“ Hb, or Hb*®
Hb*.
The set of alleles present in an individual for a given gene is known as the
individual’s genotype. The three combinations of two alleles above are
therefore the three different genotypes. Individuals that have two copies of
the same allele are called homozygous; individuals with two different
alleles are called heterozygous. So, an individual that is Hb“ Hb“ is
homozygous normal beta chain, an individual that is Hb“ Hb is
heterozygous, and an individual that is Hb* Hb® is homozygous abnormal
beta chain.
There is one more term that you need to know: the expression of the
particular combination of alleles an individual has at a locus is known as the
individual’s phenotype. The phenotype is really nothing more than the final
end product of the genes and their interaction with the environment.
Homozygous Hb® Hb® individuals (called sickle-cell anemics) can have
many sickle-shaped (as opposed to normal disc-shaped) erythrocytes in
their blood. How does this occur? The process is well-understood, and
summarized below.
In the capillaries (microscopic blood vessels that directly exchange oxygen
with the tissues), erythrocytes can be subjected to low oxygen tension after
they lose their oxygen to the surrounding tissues. In this low oxygen
situation, the abnormal hemoglobin molecules of Hb* Hb® individuals tend
to polymerize (join together), forming stiff, tubular fibers which ultimately
distort the shape of the entire erythrocyte, giving it the characteristic
“sickle” shape. These sickled cells have a number of effects on the body via
two processes.
1. The sickle-shape affects capillary blood flow:
Sickled cells are less able to enter and move through the capillaries.
Once in the capillaries, they clog capillary flow and cause small blood
clots.
Reduced blood flow results in reduced oxygen availability to the
tissues.
Reduced oxygen supply results in tissue death and damage to vital
organs (e.g., the heart, liver and spleen).
2. Sickled blood cells have a shorter lifespan than normal red blood
cells:
Reduced lifespan of erythrocytes places a greater demand on the bone
marrow to make new red blood cells and on the spleen to break down
dead erythrocytes.
Increased demand on the bone matrow results in severe pain in the
long bones and joints.
Individuals suffering from sickle-cell anemia are frequently ill and
generally have a considerably reduced lifespan. These individuals
are said to have sickle-cell disease.
Homozygous Hb“ Hb4 individuals have erythrocytes which retain their
normal shape in the body and which retain normal shape even when blood
samples are subjected to greatly reduced oxygen tension in laboratory tests.
Heterozygous individuals (Hb“ Hb‘) are said to be carriers for sickle-cell
anemia. Note: this is a specific term and is not the same thing as sickle cell
anemia—heterozygotes do not have the disease themselves but their
children may inherit the condition. Carriers have no anemia, do have good
health (as do Hb“ Hb4 individuals) and their erythrocytes maintain normal
shape in the blood. In other words, they are phenotypically normal under
most conditions, and probably do not know that they “carry” the Hb® allele.
However, if heterozygotes are exposed to conditions of low oxygen levels
(such as strenuous activity at high altitudes) some of their erythrocytes do
sickle. Red blood cells in blood samples of heterozygotes subjected to
greatly reduced oxygen tension in the laboratory also sickle.
Why is sickle cell anemia most prevalent in people with origins in Central
Africa and the Mediterranean? If you look at the figure below ({link]) , you
will see the occurrence of sickle cell anemia overlaps with the
pervasiveness of malaria. This seems odd, but those individuals how are
heterozygous (Hb“ Hb‘) for the sickle cell allele are less likely to contract
and die from malaria then those who are homozygous (Hb“ Hb“). The Hb
polypeptide that is produced by the heterozygous individual stops the
organism (Plasmodium) that causes malaria from invading the red blood
cells. So, in areas where malaria is common there is selection pressure for
the Hb® allele, and the Hb® allele occurs in a higher frequency because the
those who have one copy of the Hb® allele will live longer and have more
children. In areas where malaria is not common, there is selection pressure
against the Hb® allele, and the Hb® allele occurs in a lower frequency. As
you will learn in a later chapter, there is an 25% chance that two carriers
will have a child who is homozygous Hb® Hb‘), and this child will pay the
evolutionary price for the protection from malaria that the parents were
afforded. Hopefully, you will now understand how evolution favors the
presence of such a potentially detrimental allele in a population. The sickle
cell example is only one of what is called heterozygous advantage, we have
provided a number of other examples in [link].
The hatched line represents the distribution of malaria. The various red
colors represent the relative frequency of sickle cell allele in the
population with the dark red having the highest frequency and the light
red having the lowest frequency. Work by Eva Horne.
Recessive
Illness
Cystic fibrosis
G6PD
Deficiency
Phenylketonuria
(PKU)
Tay-Sachs
disease
Noninsulin-
dependent
diabetes
mellitus
Heterozygote
Advantage
protection
against diarrheal
diseases such as
cholera
Protection
against malaria
Protection
against
miscarriage
induced by a
fungal toxin
Protection
against
tuberculosis
Protection
against
starvation
Possible Explanation
Carriers have too few
functional chloride
channels in intestinal
cells, blocking toxin
Red blood cells
inhospitable to malaria
Excess amino acid
(phenylalanine) in carriers
inactivates toxin
Unknown
Tendency to gain weight
protects against starvation
during famine
Examples of Heterozygous Advantage in Humans
Sexual Reproduction
Introduction
"Being the inventor of sex would seem to be a sufficient distinction for a
creature just barely large enough to be seen by the naked eye. [Comment
about Volvox, a freshwater green algae, which appears indetermimately
plantlike and animal-like during its reproductive cycle.] " Joseph Wood
Krutch, 1957
Sexual reproduction was an early evolutionary innovation after the
appearance of eukaryotic cells. The fact that most eukaryotes reproduce
sexually is evidence of its evolutionary success. In many animals, it is the
only mode of reproduction. And yet, scientists recognize some real
disadvantages to sexual reproduction. On the surface, offspring that are
genetically identical to the parent may appear to be more advantageous. If
the parent organism is successfully occupying a habitat, offspring with the
same traits would be similarly successful. There is also the obvious benefit
to an organism that can produce offspring by asexual budding,
fragmentation, or asexual eggs. These methods of reproduction do not
require another organism of the opposite sex. There is no need to expend
energy finding or attracting a mate. That energy can be spent on producing
more offspring. Indeed, some organisms that lead a solitary lifestyle have
retained the ability to reproduce asexually. In addition, asexual populations
only have female individuals, so every individual is capable of
reproduction. In contrast, the males in sexual populations (half the
population) are not producing offspring themselves. Because of this, an
asexual population can grow twice as fast as a sexual population in theory.
This means that in competition, the asexual population would have the
advantage. All of these advantages to asexual reproduction, which are also
disadvantages to sexual reproduction, should mean that the number of
species with asexual reproduction should be more common.
However, multicellular organisms that exclusively depend on asexual
reproduction are exceedingly rare. Why is sexual reproduction so common?
This is one of the important questions in biology and has been the focus of
much research from the latter half of the twentieth century until now. A
likely explanation is that the variation that sexual reproduction creates
among offspring is very important to the survival and reproduction of those
offspring. The only source of variation in asexual organisms is mutation.
This is the ultimate source of variation in sexual organisms. In addition,
those different mutations are continually reshuffled from one generation to
the next when different parents combine their unique genomes, and the
genes are mixed into different combinations by the process of meiosis.
Meiosis is the division of the contents of the nucleus that divides the
chromosomes among gametes. Variation is introduced during meiosis, as
well as when the gametes combine in fertilization.
Note:
Evolution in Action
The Red Queen Hypothesis
There is no question that sexual reproduction provides evolutionary
advantages to organisms that employ this mechanism to produce offspring.
The problematic question is why, even in the face of fairly stable
conditions, sexual reproduction persists when it is more difficult and
produces fewer offspring for individual organisms? Variation is the
outcome of sexual reproduction, but why are ongoing variations necessary?
Enter the Red Queen hypothesis, first proposed by Leigh Van Valen in
1973, {footnote The concept was named in reference to the Red Queen's race
in Lewis Carroll's book, Through the Looking-Glass, in which the Red
Queen says one must run at full speed just to stay where one is.
Leigh Van Valen, “A new evolutionary law,” Evolutionary Theory 1
(1973): 1-30.
All species coevolve with other organisms. For example, predators
coevolve with their prey, and parasites coevolve with their hosts. A
remarkable example of coevolution between predators and their prey is the
unique coadaptation of night flying bats and their moth prey. Bats find their
prey by emitting high-pitched clicks, but moths have evolved simple ears
to hear these clicks so they can avoid the bats. The moths have also
adapted behaviors, such as flying away from the bat when they first hear it,
or dropping suddenly to the ground when the bat is upon them. Bats have
evolved “quiet” clicks in an attempt to evade the moth’s hearing. Some
moths have evolved the ability to respond to the bats’ clicks with their own
clicks as a strategy to confuse the bats echolocation abilities.
Each tiny advantage gained by favorable variation gives a species an edge
over close competitors, predators, parasites, or even prey. The only method
that will allow a coevolving species to keep its own share of the resources
is also to continually improve its ability to survive and produce offspring.
AS one species gains an advantage, other species must also develop an
advantage or they will be outcompeted. No single species progresses too
far ahead because genetic variation among progeny of sexual reproduction
provides all species with a mechanism to produce adapted individuals.
Species whose individuals cannot keep up become extinct. The Red
Queen’s catchphrase was, “It takes all the running you can do to stay in the
same place.” This is an apt description of coevolution between competing
species.
Life Cycles of Sexually Reproducing Organisms
Fertilization and meiosis alternate in sexual life cycles. What happens
between these two events depends on the organism. The process of meiosis
reduces the resulting gamete’s chromosome number by half. Fertilization,
the joining of two haploid gametes, restores the diploid condition. The
number of sets of chromosomes in a cell is called its ploidy level. Haploid
(1n) cells contain one set of chromosomes. Cells containing two sets of
chromosomes are called diploid (2n). There are three main categories of life
cycles in multicellular organisms: diploid-dominant, in which the
multicellular diploid stage is the most obvious life stage (and there is no
multicellular haploid stage), as with most animals including humans;
haploid-dominant, in which the multicellular haploid stage is the most
obvious life stage (and there is no multicellular diploid stage), as with all
fungi and some algae; and alternation of generations, in which the two
stages, haploid and diploid, are apparent to one degree or another depending
on the group, as with plants and some algae.
Nearly all animals employ a diploid-dominant life-cycle strategy in which
the only haploid cells produced by the organism are the gametes. The
gametes are produced from diploid germ cells, a special cell line that only
produces gametes. Once the haploid gametes are formed, they lose the
ability to divide again. There is no multicellular haploid life stage.
Fertilization occurs with the fusion of two gametes, usually from different
individuals, restoring the diploid state ({link]a).
Note:
Zygospore
ities
ASEXUAL
(a) In animals, sexually reproducing
adults form haploid gametes from
diploid germ cells. (b) Fungi, such as
black bread mold (Rhizopus
nigricans), have haploid-dominant life
cycles. (c) Plants have a life cycle that
alternates between a multicellular
haploid organism and a multicellular
diploid organism. (credit c “fern”:
modification of work by Cory Zanker;
credit c “gametophyte”: modification
of work by “VImastra”/Wikimedia
Commons)
Most fungi and algae employ a life-cycle strategy in which the multicellular
“body” of the organism is haploid. During sexual reproduction, specialized
haploid cells from two individuals join to form a diploid zygote. The zygote
immediately undergoes meiosis to form four haploid cells called spores
([link]b).
The third life-cycle type, employed by some algae and all plants, is called
alternation of generations. These species have both haploid and diploid
multicellular organisms as part of their life cycle. The haploid multicellular
plants are called gametophytes because they produce gametes. Meiosis is
not involved in the production of gametes in this case, as the organism that
produces gametes is already haploid. Fertilization between the gametes
forms a diploid zygote. The zygote will undergo many rounds of mitosis
and give rise to a diploid multicellular plant called a sporophyte.
Specialized cells of the sporophyte will undergo meiosis and produce
haploid spores. The spores will develop into the gametophytes ({link]c).
Meiosis
Introduction
"T may finally call attention to the probability that the association of the
paternal and maternal chromosomes in pairs, and their subsequent
separation during the reducing division as indicated above, may constitute
the physical basis of the Mendelian law of heredity." Walter S. Sutton, "On
the Morphology of the Chromosome Group in Brachystola
magna",Biological Bulletin, 1902, 4:39
Sutton was one of the biologists (along with Theodor Boveri) who
discovered that chromosomes correspond to the paired "particles" required
by Mendel's Laws, and that the number of these chromosomes is halved at
the time that sperm and egg cells are generated. The Boveri-Sutton
Chromosome Theory (also known as the Chromosome Theory of
Inheritance) is one of the important linkages between Mendel and modern
molecular biology. Sutton was raised on a farm near Russell, Kansas, and
played basketball under Coach Naismith at the University of Kansas. His
ground-breaking work was done at Columbia University in New York City.
So when you study meiosis and heredity, remember that a major part of this
knowledge came from the work of another biologist from Kansas, Walter
Sutton, working with grasshoppers (the aforementioned Brachystola
magna) that are indigenous to the state of Kansas.
Haploid (1n)
Gametes Diploid (2n)
Somatic cell
ie
Fertilization
a
Homologous Pair
of chromosomes
The process of fertilization produces a dipliod cell by the union of two
haploid cells. The homologous pairs are based on size and the color
refers to the maternal and paternal chromosomes. Work by Robbie
Bear.
Sexual reproduction requires fertilization, a union of two cells from two
individual organisms. If those two cells each contain one set of
chromosomes, then the resulting cell contains two sets of chromosomes.
The number of sets of chromosomes in a cell is called its ploidy level.
Haploid (1n) cells contain one set of chromosomes. Cells containing two
sets of chromosomes are called diploid (2n) ({link]). If the reproductive
cycle is to continue, the diploid cell must somehow reduce its number of
chromosome sets before fertilization can occur again, or there will be a
continual doubling in the number of chromosome sets in every generation.
So, in addition to fertilization, sexual reproduction includes a nuclear
division, known as meiosis, that reduces the number of chromosome sets.
Most animals and plants are diploid, containing two sets of chromosomes;
in each somatic cell (the nonreproductive cells of a multicellular organism),
the nucleus contains two copies of each chromosome that are referred to as
homologous chromosomes ({link]). Somatic cells are sometimes referred
to as “body” cells. Homologous chromosomes are matched pairs containing
genes for the same traits in identical locations along their length. Diploid
organisms inherit one copy of each homologous chromosome from each
parent; all together, they are considered a full set of chromosomes. In
animals, haploid cells containing a single copy of each homologous
chromosome are found only within gametes. Gametes fuse with another
haploid gamete to produce a diploid cell.
Diploid (2n) Diploid (2n)
Germ cell Germ cell
DNA Replication and
Chromosome Duplication
7»
Homologous pair
of chromosomes Homologous pair of
duplicated chromosomes
each consisting of sister
chromatids
The process of DNA replication produces a duplicated chromosome
with two sister chromatids in each of the homologous pairs. The
homologous pairs are based on size and the color refers to the maternal
and paternal chromosomes. Work by Robbie Bear.
The nuclear division that forms haploid cells, which is called meiosis, is
related to mitosis. As you have learned, mitosis is part of a cell reproduction
cycle that results in identical daughter nuclei that are also genetically
identical to the original parent nucleus. In mitosis, both the parent and the
daughter nuclei contain the same number of chromosome sets—diploid for
most plants and animals. Meiosis employs many of the same mechanisms
as mitosis. However, the starting nucleus is always diploid and the nuclei
that result at the end of a meiotic cell division are haploid. To achieve the
reduction in chromosome number, meiosis consists of one round of
chromosome duplication ([link]) and two rounds of nuclear division.
Because the events that occur during each of the division stages are
analogous to the events of mitosis, the same stage names are assigned.
However, because there are two rounds of division, the stages are
designated with a “I” or “II.” Thus, meiosis I is the first round of meiotic
division and consists of prophase I, metaphase I, and so on. Meiosis I
reduces the number of chromosome sets from two to one. The genetic
information is also mixed during this division to create unique recombinant
chromosomes. Meiosis II, in which the second round of meiotic division
takes place in a way that is similar to mitosis, includes prophase II,
pmetaphase IJ, and so on ((link]).
yng
G1
centrioles
nucleus
DNA replication =
Un-replicated, Replicated,
uncondensed uncondensed
DNA
Meiosis |: Products
2 haploid cells
Meiosis Il: Prophase 2
)
Meiosis Il: Metaphase 2 Meiosis Il: Anaphase 2
Meiosis |: Prophase 1 Meiosis |: Metaphase 1
spindle fibers
£6
Homologous pair of
condensed, replicated
chromosomes in synapsis
Meiosis |: Telophase 1
‘G ‘
Meiosis II: Telophase 2
Meiosis |: Anaphase 1
Meiosis II: Products
4 haploid cells = gametes
ee Of
This image illustrates meiosis for a cell with 2 pairs of homologous
chromosomes. The homologous pairs are based on size and the color
refers to the maternal and paternal chromosomes. Work by Eva Horne.
Interphase
Meiosis is preceded by an interphase consisting of the Gj, S, and Gp phases,
which are nearly identical to the phases preceding mitosis. The G, phase is
the first phase of interphase and is focused on cell growth. In the S phase,
the DNA of the chromosomes is replicated. Finally, in the G» phase, the cell
undergoes the final preparations for meiosis.
During DNA duplication of the S phase, each chromosome becomes
composed of two identical copies (called sister chromatids) that are held
together at the centromere until they are pulled apart during meiosis II. In
an animal cell, the centrosomes that organize the microtubules of the
meiotic spindle also replicate. This prepares the cell for the first meiotic
phase.
Meiosis I
In prophase I, the chromosomes can be seen clearly microscopically. As the
nuclear envelope begins to break down, the proteins associated with
homologous chromosomes bring the pair close to each other. The tight
pairing of the homologous chromosomes is called synapsis. In synapsis, the
genes on the chromatids of the homologous chromosomes are precisely
aligned with each other. An exchange of chromosome segments between
non-sister homologous chromatids occurs and is called crossing over.
The crossover events are the first source of genetic variation produced by
meiosis. A single crossover event between homologous non-sister
chromatids leads to a reciprocal exchange of equivalent DNA between a
maternal chromosome and a paternal chromosome. Now, when that sister
chromatid is moved into a gamete, it will carry some DNA from one parent
of the individual and some DNA from the other parent. The recombinant
sister chromatid has a combination of maternal and paternal genes that did
not exist before the crossover. In the next class period, we will explore how
crossing over and recombinant sister chromatids influence patterns of
inheritance.
The key event in metaphase I is the attachment of the spindle fiber
microtubules to the kinetochore proteins at the centromeres. The
microtubules assembled from centrosomes at opposite poles of the cell
grow toward the middle of the cell. The homologous chromosomes are held
together and form a tetrad. At the end of metaphase I, each tetrad is
attached to microtubules from both poles, with one homologous
chromosome attached at one pole and the other homologous chromosome
attached to the other pole. In addition, the nuclear membrane has broken
down entirely.
By the end metaphase I, the homologous chromosomes are arranged in the
center of the cell with the kinetochores facing opposite poles. The
orientation of each pair of homologous chromosomes at the center of the
cell is random.
This randomness, called independent assortment, is the physical basis for
the generation of the second form of genetic variation in offspring. Consider
that the homologous chromosomes of a sexually reproducing organism are
originally inherited as two separate sets, one from each parent. Using
humans as an example, one set of 23 chromosomes is present in the egg
donated by the mother. The father provides the other set of 23 chromosomes
in the sperm that fertilizes the egg. In metaphase I, these pairs line up at the
midway point between the two poles of the cell. Because there is an equal
chance that a microtubule fiber will encounter a maternally or paternally
inherited chromosome, the arrangement of the tetrads at the metaphase plate
is random. Any maternally inherited chromosome may face either pole.
Any paternally inherited chromosome may also face either pole. The
orientation of each tetrad is independent of the orientation of the other 22
tetrads.
In each cell that undergoes meiosis, the arrangement of the tetrads is
different. The number of variations depends on the number of chromosomes
making up a set. There are two possibilities for orientation (for each tetrad);
thus, the possible number of alignments equals 2” where n is the number of
chromosomes per set. Humans have 23 chromosome pairs, which results in
over eight million (27) possibilities. This number does not include the
variability previously created in the sister chromatids by crossover. Given
these two mechanisms, it is highly unlikely that any two haploid cells
resulting from meiosis will have the same genetic composition ((Link]).
To summarize the genetic consequences of meiosis I: the maternal and
paternal genes are recombined by crossover events occurring on each
homologous pair during prophase I; in addition, the random assortment of
tetrads at metaphase produces a unique combination of maternal and
paternal chromosomes that will make their way into the gametes.
Possible Chromosome Arrangement | Possible Chromosome Arrangement II
Meiosis |: Homologous
chromosomes separate
Meiosis |: Homologous
chromosomes separate
Meiosis II: Sister
chromatids separate
Meiosis Il: Sister
chromatids separate
This illustration shows that, in a cell with 2 pairs of
homologous chromosomes, 2 possible arrangements of
chromosomes in Meiosis I will give rise to 4 different
kinds of gametes. These are shown at the bottom of the
figure; although there are 8 total gametes, there are 4
pairs that are identical.
In anaphase I, the spindle fibers pull the homologous chromosomes apart.
The sister chromatids remain tightly bound together at the centromere
({link]).
In telophase I, the separated chromosomes arrive at opposite poles. The
remainder of the typical telophase events may or may not occur depending
on the species. In some organisms, the chromosomes decondense and
nuclear envelopes form around the chromatids in telophase I.
Cytokinesis, the physical separation of the cytoplasmic components into
two daughter cells, occurs without reformation of the nuclei in other
organisms. In nearly all species, cytokinesis separates the cell contents by
either a cleavage furrow (in animals and some fungi), or a cell plate that
will ultimately lead to formation of cell walls that separate the two daughter
cells (in plants). At each pole, there is just one member of each pair of the
homologous chromosomes, so only one full set of the chromosomes is
present. This is why the cells are considered haploid—there is only one
chromosome set, even though there are duplicate copies of the set because
each homolog still consists of two sister chromatids that are still attached to
each other. However, although the sister chromatids were once duplicates of
the same chromosome, they are no longer identical at this stage because of
crossovers.
Meiosis II
In meiosis II, the connected sister chromatids remaining in the haploid cells
from meiosis I will be split to form four haploid cells ([link]). In some
species, cells enter a brief interphase, or interkinesis, that lacks an S phase,
before entering meiosis II. Chromosomes are not duplicated during
interkinesis. The two cells produced in meiosis I go through the events of
meiosis II in synchrony. Overall, meiosis II resembles the mitotic division
of a haploid cell.
In prophase II, if the chromosomes decondensed in telophase I, they
condense again. If nuclear envelopes were formed, they fragment into
vesicles. The centrosomes duplicated during interkinesis move away from
each other toward opposite poles, and new spindles are formed. In early
metaphase IT, the nuclear envelopes are completely broken down, and the
spindle is fully formed. Each sister chromatid forms an individual
kinetochore that attaches to microtubules from opposite poles. In metaphase
II, the sister chromatids are maximally condensed and aligned at the center
of the cell. In anaphase II, the sister chromatids are pulled apart by the
spindle fibers and move toward opposite poles.
In telophase II, the chromosomes arrive at opposite poles and begin to
decondense. Nuclear envelopes form around the chromosomes. Cytokinesis
separates the two cells into four genetically unique haploid cells. At this
point, the nuclei in the newly produced cells are both haploid and have only
one copy of the single set of chromosomes. The cells produced are
genetically unique because of the random assortment of paternal and
maternal homologs and because of the recombination of maternal and
paternal segments of chromosomes—with their sets of genes—that occurs
during crossover.
Mendel’s Experiments
Introduction
""Mendel's forty-odd year stint at the Brno abbey was, indeed, deeply
constrained by rules, habits, and limits. He began his experiments on
inheritance by breeding field mice but was asked to discontinue them
because forcing mice to mate was considered too risqué for a monk."" S.
Mukherjee, "On Tenderness", introduction to The Best American Science
and Nature Writing, Mariner Press, Boston and New York, 2013
Johann Gregor Mendel
set the framework for
the study of genetics.
Johann Gregor Mendel (1822-1884) ([link]) was a lifelong learner, teacher,
scientist, and man of faith. As a young adult, he joined the Augustinian
Abbey of St. Thomas in Bmo in what is now the Czech Republic.
Supported by the monastery, he taught physics, botany, and natural science
courses at the secondary and university levels. In 1856, he began a decade-
long research pursuit involving inheritance patterns in honeybees and
plants, ultimately settling on pea plants as his primary model system (a
system with convenient characteristics that is used to study a specific
biological phenomenon to gain understanding to be applied to other
systems). In 1865, Mendel presented the results of his experiments with
nearly 30,000 pea plants to the local natural history society. He
demonstrated that traits are transmitted faithfully from parents to offspring
in specific patterns. In 1866, he published his work, Experiments in Plant
Hybridization, 2"! in the proceedings of the Natural History Society of
Brunn.
Johann Gregor Mendel, “Versuche iiber Pflanzenhybriden.” Verhandlungen
des naturforschenden Vereines in Brtinn, Bd. IV fiir das Jahr, 1865
Abhandlungen (1866):3—47. [for English translation, see
http://www.mendelweb.org/Mendel.plain.html]
Mendel’s work went virtually unnoticed by the scientific community, which
incorrectly believed that the process of inheritance involved a blending of
parental traits that produced an intermediate physical appearance in
offspring. This hypothetical process appeared to be correct because of what
we know now as continuous variation. Continuous variation is the range of
small differences we see among individuals in a characteristic like human
height. It does appear that offspring are a “blend” of their parents’ traits
when we look at characteristics that exhibit continuous variation. Mendel
worked instead with traits that show discontinuous variation. Discontinuous
variation is the variation seen among individuals when each individual
shows one of two—or a very few—easily distinguishable traits, such as
violet or white flowers. Mendel’s choice of these kinds of traits allowed him
to see experimentally that the traits were not blended in the offspring as
would have been expected at the time, but that they were inherited as
distinct traits. In 1868, Mendel became abbot of the monastery and
exchanged his scientific pursuits for his pastoral duties. He was not
recognized for his extraordinary scientific contributions during his lifetime;
in fact, it was not until 1900 that his work was rediscovered, reproduced,
and revitalized by scientists on the brink of discovering the chromosomal
basis of heredity.
Mendel’s Crosses
Mendel’s seminal work was accomplished using the garden pea, Pisum
sativum, to study inheritance. This species naturally self-fertilizes, meaning
that pollen encounters ova within the same flower. The flower petals remain
sealed tightly until pollination is completed to prevent the pollination of
other plants. The result is highly inbred, or “true-breeding,” pea plants.
These are plants that always produce offspring that look like the parent. By
experimenting with true-breeding pea plants, Mendel avoided the
appearance of unexpected traits in offspring that might occur if the plants
were not true breeding. The garden pea also grows to maturity within one
season, meaning that several generations could be evaluated over a
relatively short time. Finally, large quantities of garden peas could be
cultivated simultaneously, allowing Mendel to conclude that his results did
not come about simply by chance.
Mendel performed hybridizations, which involve mating two true-breeding
individuals that have different traits. In the pea, which is naturally self-
pollinating, this is done by manually transferring pollen from the anther of a
mature pea plant of one variety to the stigma of a separate mature pea plant
of the second variety.
Plants used in first-generation crosses were called P, or parental generation,
plants ([link]). Mendel collected the seeds produced by the P plants that
resulted from each cross and grew them the following season. These
offspring were called the Fj, or the first filial (filial = daughter or son),
generation. Once Mendel examined the characteristics in the F; generation
of plants, he allowed them to self-fertilize naturally. He then collected and
grew the seeds from the F, plants to produce the Fy, or second filial,
generation. Mendel’s experiments extended beyond the F> generation to the
F3 generation, F, generation, and so on, but it was the ratio of
characteristics in the P, F;, and F> generations that were the most intriguing
and became the basis of Mendel’s postulates.
Hybridization of true-breeding plants
Self-fertilization of hybrid plants
Mendel’s process for performing
crosses included examining flower
color.
Garden Pea Characteristics Revealed the Basics of Heredity
In his 1865 publication, Mendel reported the results of his crosses involving
seven different characteristics, each with two contrasting traits. A trait is
defined as a variation in the physical appearance of a heritable
characteristic. The characteristics included plant height, seed texture, seed
color, flower color, pea-pod size, pea-pod color, and flower position. For
the characteristic of flower color, for example, the two contrasting traits
were white versus violet. To fully examine each characteristic, Mendel
generated large numbers of F, and F> plants and reported results from
thousands of F> plants.
What results did Mendel find in his crosses for flower color? First, Mendel
confirmed that he was using plants that bred true for white or violet flower
color. Irrespective of the number of generations that Mendel examined, all
self-crossed offspring of parents with white flowers had white flowers, and
all self-crossed offspring of parents with violet flowers had violet flowers.
In addition, Mendel confirmed that, other than flower color, the pea plants
were physically identical. This was an important check to make sure that
the two varieties of pea plants only differed with respect to one trait, flower
color.
Once these validations were complete, Mendel applied the pollen from a
plant with violet flowers to the stigma of a plant with white flowers. After
gathering and sowing the seeds that resulted from this cross, Mendel found
that 100 percent of the F; hybrid generation had violet flowers.
Conventional wisdom at that time would have predicted the hybrid flowers
to be pale violet or for hybrid plants to have equal numbers of white and
violet flowers. In other words, the contrasting parental traits were expected
to blend in the offspring. Instead, Mendel’s results demonstrated that the
white flower trait had completely disappeared in the F; generation.
Importantly, Mendel did not stop his experimentation there. He allowed the
F, plants to self-fertilize and found that 705 plants in the Fy generation had
violet flowers and 224 had white flowers. This was a ratio of 3.15 violet
flowers to one white flower, or approximately 3:1. When Mendel
transferred pollen from a plant with violet flowers to the stigma of a plant
with white flowers and vice versa, he obtained approximately the same ratio
irrespective of which parent—male or female—contributed which trait.
This is called a reciprocal cross —a paired cross in which the respective
traits of the male and female in one cross become the respective traits of the
female and male in the other cross. For the other six characteristics that
Mendel examined, the F, and F> generations behaved in the same way that
they behaved for flower color. One of the two traits would disappear
completely from the F, generation, only to reappear in the F> generation at
a ratio of roughly 3:1 ({link]). He wrote, in the typically sparse prose of a
scientist, "In this generation, along with the dominating traits, the recessive
ones also reappear, their individuality fully revealed, and they do so in the
decisively expressed average proportion of 3:1, so that among each four
plants of this generation three receive the dominating and one the recessive
characteristic." (Gregor Mendel, 'Experiments on Plant Hybrids', 1865)
Seed shape -) ae)
Round Wrinkled
Seed color ~) ww
Flower position
Yellow Green
— - y
Flower color ») (ob Axial Terminal
Purple White
Pod shape Jf J
Inflated Constricted
Stem height
Pod color
Yellow Green Tall Dwarf
Mendel identified seven pea plant characteristics.
Upon compiling his results for many thousands of plants, Mendel
concluded that the characteristics could be divided into expressed and latent
traits. He called these dominant and recessive traits, respectively.
Dominant traits are those that are inherited unchanged in a hybridization.
Recessive traits become latent, or disappear in the offspring of a
hybridization. The recessive trait does, however, reappear in the progeny of
the hybrid offspring. An example of a dominant trait is the violet-colored
flower trait. For this same characteristic (flower color), white-colored
flowers are a recessive trait. The fact that the recessive trait reappeared in
the F> generation meant that the traits remained separate (and were not
blended) in the plants of the F; generation. Mendel proposed that this was
because the plants possessed two copies of the trait for the flower-color
characteristic, and that each parent transmitted one of their two copies to
their offspring, where they came together. Moreover, the physical
observation of a dominant trait could mean that the genetic composition of
the organism included two dominant versions of the characteristic, or that it
included one dominant and one recessive version. Conversely, the
observation of a recessive trait meant that the organism lacked any
dominant versions of this characteristic.
Laws of Inheritance
Introduction
"If A denotes one of the two constant traits, for example, the dominating
one, a the recessive, and the Aa the hybrid form in which both are united,
then the expression: A + 2Aa + a gives the series for the progeny of plants
hybrid in a pair of differing traits. " Gregor Mendel, 1865
The seven characteristics that Mendel evaluated in his pea plants were each
expressed as one of two versions, or traits. Mendel deduced from his results
that each individual had two discrete copies of the characteristic that are
passed individually to offspring. We now call those two copies genes, which
are carried on chromosomes. The reason we have two copies of each gene
is that we inherit one from each parent. In fact, it is the chromosomes we
inherit and the two copies of each gene are located on paired chromosomes.
Recall that in meiosis these chromosomes are separated out into haploid
gametes. This separation, or segregation, of the homologous chromosomes
means also that only one of the copies of the gene gets moved into a
gamete. The offspring are formed when that gamete unites with one from
another parent and the two copies of each gene (and chromosome) are
restored.
For cases in which a single gene controls a single characteristic, a diploid
organism has two genetic copies that may or may not encode the same
version of that characteristic. For example, one individual may carry a gene
that determines white flower color and a gene that determines violet flower
color. Gene variants that arise by mutation and exist at the same relative
locations on homologous chromosomes are called alleles. Mendel examined
the inheritance of genes with just two allele forms, but it is common to
encounter more than two alleles for any given gene in a natural population.
Phenotypes and Genotypes
Two alleles for a given gene in a diploid organism are expressed and
interact to produce physical characteristics. The observable traits expressed
by an organism are referred to as its phenotype. An organism’s underlying
genetic makeup, consisting of both the physically visible and the non-
expressed alleles, is called its genotype. Mendel’s hybridization
experiments demonstrate the difference between phenotype and genotype.
For example, the phenotypes that Mendel observed in his crosses between
pea plants with differing traits are connected to the diploid genotypes of the
plants in the P, F,, and F> generations. We will use a second trait that
Mendel investigated, seed color, as an example. Seed color is governed by a
single gene with two alleles. The yellow-seed allele is dominant and the
green-seed allele is recessive. When true-breeding plants were cross-
fertilized, in which one parent had yellow seeds and one had green seeds,
all of the F; hybrid offspring had yellow seeds. That is, the hybrid offspring
were phenotypically identical to the true-breeding parent with yellow seeds.
However, we know that the allele donated by the parent with green seeds
was not simply lost because it reappeared in some of the F> offspring
({link]). Therefore, the F,; plants must have been genotypically different
from the parent with yellow seeds.
The P plants that Mendel used in his experiments were each homozygous
for the trait he was studying. Diploid organisms that are homozygous for a
gene have two identical alleles, one on each of their homologous
chromosomes. The genotype is often written as YY or yy, for which each
letter represents one of the two alleles in the genotype. The dominant allele
is capitalized and the recessive allele is lower case. The letter used for the
gene (seed color in this case) is usually related to the dominant trait (yellow
allele, in this case, or “Y”). Mendel’s parental pea plants always bred true
because both produced gametes carried the same allele. When P plants with
contrasting traits were cross-fertilized, all of the offspring were
heterozygous for the contrasting trait, meaning their genotype had different
alleles for the gene being examined. For example, the F; yellow plants that
received a Y allele from their yellow parent and a y allele from their green
parent had the genotype Yy.
Phenotype
[P] at @
(a) Cross-fertilization
:
100 percent
[Fa]
yellow progeny
(hybrids)
.)
y (b) Self-fertilization
‘*) 75 percent
© yellow
progeny
25 percent
green
progeny
Genotype
[Pp] yy “Ts YY
(a) Cross-fertilization
[F:]
1
00 ae (yellow)
uv (b) Self-fertilization
25 percent
WAC
(yellow)
50 percent
Yy
25 percent
y } (green)
Phenotypes are physical expressions of traits that
are transmitted by alleles. Capital letters represent
dominant alleles and lowercase letters represent
recessive alleles. The phenotypic ratios are the
ratios of visible characteristics. The genotypic
ratios are the ratios of gene combinations in the
offspring, and these are not always distinguishable
in the phenotypes.
Law of Dominance
Our discussion of homozygous and heterozygous organisms brings us to
why the F, heterozygous offspring were identical to one of the parents,
rather than expressing both alleles. In all seven pea-plant characteristics,
one of the two contrasting alleles was dominant, and the other was
recessive. Mendel called the dominant allele the expressed unit factor; the
recessive allele was referred to as the latent unit factor. We now know that
these so-called unit factors are actually genes on homologous
chromosomes. For a gene that is expressed in a dominant and recessive
pattern, homozygous dominant and heterozygous organisms will look
identical (that is, they will have different genotypes but the same
phenotype), and the recessive allele will only be observed in homozygous
recessive individuals ({link]).
Correspondence between Genotype and Phenotype for a
Dominant-Recessive Characteristic.
Homozygous Heterozygous Homozygous
Genotype YY Yy yy
Phenotype yellow yellow green
Mendel’s law of dominance states that in a heterozygote, one trait will
conceal the presence of another trait for the same characteristic. For
example, when crossing true-breeding violet-flowered plants with true-
breeding white-flowered plants, all of the offspring were violet-flowered,
even though they all had one allele for violet and one allele for white.
Rather than both alleles contributing to a phenotype, the dominant allele
will be expressed exclusively. The recessive allele will remain latent, but
will be transmitted to offspring in the same manner as that by which the
dominant allele is transmitted. The recessive trait will only be expressed by
offspring that have two copies of this allele ([link]), and these offspring will
breed true when self-crossed.
The allele for albinism,
expressed here in humans, is
recessive. Both of this
child’s parents carried the
recessive allele.
Monohybrid Cross and the Punnett Square
When fertilization occurs between two true-breeding parents that differ by
only the characteristic being studied, the process is called a monohybrid
cross, and the resulting offspring are called monohybrids. Mendel
performed seven types of monohybrid crosses, each involving contrasting
traits for different characteristics. Out of these crosses, all of the F,
offspring had the phenotype of one parent, and the F> offspring had a 3:1
phenotypic ratio. On the basis of these results, Mendel postulated that each
parent in the monohybrid cross contributed one of two paired unit factors to
each offspring, and every possible combination of unit factors was equally
likely.
The results of Mendel’s research can be explained in terms of probabilities,
which are mathematical measures of likelihood. The probability of an event
is calculated by the number of times the event occurs divided by the total
number of opportunities for the event to occur. A probability of one (100
percent) for some event indicates that it is guaranteed to occur, whereas a
probability of zero (0 percent) indicates that it is guaranteed to not occur,
and a probability of 0.5 (50 percent) means it has an equal chance of
occurring or not occurring.
To demonstrate this with a monohybrid cross, consider the case of true-
breeding pea plants with yellow versus green seeds. The dominant seed
color is yellow; therefore, the parental genotypes were YY for the plants
with yellow seeds and yy for the plants with green seeds. A Punnett
square, devised by the British geneticist Reginald Punnett, is useful for
determining probabilities because it is drawn to predict all possible
outcomes of all possible random fertilization events and their expected
frequencies. [link] shows a Punnett square for a cross between a plant with
yellow peas and one with green peas. To prepare a Punnett square, all
possible combinations of the parental alleles (the genotypes of the gametes)
are listed along the top (for one parent) and side (for the other parent) of a
grid. The combinations of egg and sperm gametes are then made in the
boxes in the table on the basis of which alleles are combining. Each box
then represents the diploid genotype of a zygote, or fertilized egg. Because
each possibility is equally likely, genotypic ratios can be determined from a
Punnett square. If the pattern of inheritance (dominant and recessive) is
known, the phenotypic ratios can be inferred as well. For a monohybrid
cross of two true-breeding parents, each parent contributes one type of
allele. In this case, only one genotype is possible in the F, offspring. All
offspring are Yy and have yellow seeds.
When the F, offspring are crossed with each other, each has an equal
probability of contributing either a Y or a y to the F, offspring. The result is
a 1 in 4 (25 percent) probability of both parents contributing a Y, resulting
in an offspring with a yellow phenotype; a 25 percent probability of parent
A contributing a Y and parent B ay, resulting in offspring with a yellow
phenotype; a 25 percent probability of parent A contributing a y and parent
B a, also resulting in a yellow phenotype; and a (25 percent) probability
of both parents contributing a y, resulting in a green phenotype. When
counting all four possible outcomes, there is a 3 in 4 probability of offspring
having the yellow phenotype and a 1 in 4 probability of offspring having
the green phenotype. This explains why the results of Mendel’s F>
generation occurred in a 3:1 phenotypic ratio. Using large numbers of
crosses, Mendel was able to calculate probabilities, found that they fit the
model of inheritance, and use these to predict the outcomes of other crosses.
Law of Segregation
Observing that true-breeding pea plants with contrasting traits gave rise to
F, generations that all expressed the dominant trait and F> generations that
expressed the dominant and recessive traits in a 3:1 ratio, Mendel proposed
the law of segregation. This law states that paired unit factors (genes) must
segregate equally into gametes such that offspring have an equal likelihood
of inheriting either factor. For the F> generation of a monohybrid cross, the
following three possible combinations of genotypes result: homozygous
dominant, heterozygous, or homozygous recessive. Because heterozygotes
could arise from two different pathways (receiving one dominant and one
recessive allele from either parent), and because heterozygotes and
homozygous dominant individuals are phenotypically identical, the law
supports Mendel’s observed 3:1 phenotypic ratio. The equal segregation of
alleles is the reason we can apply the Punnett square to accurately predict
the offspring of parents with known genotypes. The physical basis of
Mendel’s law of segregation is the first division of meiosis in which the
homologous chromosomes with their different versions of each gene are
segregated into daughter nuclei. This process was not understood by the
scientific community during Mendel’s lifetime ([link]).
Meiosis | Daughter
cells
Interphase Prometaphase | Anaphase |
Prophase | Metaphase | Telophase |
The first division in meiosis is shown.
Test Cross
Beyond predicting the offspring of a cross between known homozygous or
heterozygous parents, Mendel also developed a way to determine whether
an organism that expressed a dominant trait was a heterozygote or a
homozygote. Called the test cross, this technique is still used by plant and
animal breeders. In a test cross, the dominant-expressing organism is
crossed with an organism that is homozygous recessive for the same
characteristic. If the dominant-expressing organism is a homozygote, then
all F, offspring will be heterozygotes expressing the dominant trait ({link]).
Alternatively, if the dominant-expressing organism is a heterozygote, the F;
offspring will exhibit a 1:1 ratio of heterozygotes and recessive
homozygotes ([link]). The test cross further validates Mendel’s postulate
that pairs of unit factors segregate equally.
Note:
A test cross can be performed to
determine whether an organism
expressing a dominant trait is a
homozygote or a heterozygote.
Genotype Phenotype
Phenotypes Genotypes ratio ratio
This Punnett square shows the cross
between plants with yellow seeds and
green seeds. The cross between the
true-breeding P plants produces F,
heterozygotes that can be self-
fertilized. The self-cross of the F,
generation can be analyzed with a
Punnett square to predict the
genotypes of the F, generation. Given
an inheritance pattern of dominant—
recessive, the genotypic and
phenotypic ratios can then be
determined.
Law of Independent Assortment
Mendel’s law of independent assortment states that genes do not
influence each other with regard to the sorting of alleles into gametes, and
every possible combination of alleles for every gene is equally likely to
occur. Independent assortment of genes can be illustrated by the dihybrid
cross, a cross between two true-breeding parents that express different traits
for two characteristics. Consider the characteristics of seed color and seed
texture for two pea plants, one that has wrinkled, green seeds (rryy) and
another that has round, yellow seeds (RRYY). Because each parent is
homozygous, the law of segregation indicates that the gametes for the
wrinkled—green plant all are ry, and the gametes for the round—yellow plant
are all RY. Therefore, the F, generation of offspring all are RrYy ([link)).
Note:
A dihybrid cross in pea plants involves the genes
for seed color and texture. The P cross produces
F, offspring that are all heterozygous for both
characteristics. The resulting 9:3:3:1 F>
phenotypic ratio is obtained using a Punnett
square.
The gametes produced by the F individuals must have one allele from each
of the two genes. For example, a gamete could get an R allele for the seed
shape gene and either a Y or ay allele for the seed color gene. It cannot get
both an R and an r allele; each gamete can have only one allele per gene.
The law of independent assortment states that a gamete into which an r
allele is sorted would be equally likely to contain either a Y or ay allele.
Thus, there are four equally likely gametes that can be formed when the
RrYy heterozygote is self-crossed, as follows: RY, rY, Ry, and ry. Arranging
these gametes along the top and left of a 4 x 4 Punnett square ([link]) gives
us 16 equally likely genotypic combinations. From these genotypes, we find
a phenotypic ratio of 9 round—yellow:3 round—green:3 wrinkled—yellow:1
wrinkled—green ([{link]). These are the offspring ratios we would expect,
assuming we performed the crosses with a large enough sample size.
The physical basis for the law of independent assortment also lies in
meiosis I, in which the different homologous pairs line up in random
orientations. Each gamete can contain any combination of paternal and
maternal chromosomes (and therefore the genes on them) because the
orientation of tetrads on the metaphase plane is random ([link]).
Metaphase | _
Metaphase II
Gametes
i
a
:
:
a
:
iS
é
Metaphase II
Chromosome Arrangement 2
© Gametes ©
Genetic Genetic
arrangement 3 arrangement 4
The random segregation into daughter nuclei that
happens during the first division in meiosis can lead to a
variety of possible genetic arrangements.
Extensions of the Laws of Inheritance
Introduction
"Certain students of genetics inferred that the Mendelian units responsible
for the selected character were genes producing only a single effect. This
was careless logic. It took a good deal of hammering to get rid of this
erroneous idea. As facts accumulated it became evident that each gene
produces not a single effect, but in some cases a multitude of effects on the
characters of the individual. It is true that in most genetic work only one of
these character-effects is selected for study—the one that is most sharply
defined and separable from its contrasted character—but in most cases
minor differences also are recognizable that are just as much the product of
the same gene as is the major effect. " Thomas Hunt Morgan, 1935
Mendel studied traits with only one mode of inheritance, and one very
obvious phenotype, in pea plants. The inheritance of the traits he studied all
followed the relatively simple pattern of dominant and recessive alleles for
a single characteristic, and allowed him to suggest his Laws of Inheritance.
There are several important modes of inheritance, discovered after
Mendel’s work, that do not follow the dominant and recessive, single-gene
model. So mendel's Laws are not always going to predict the phenotypes
seen after doing a genetic cross.
Alternatives to Dominance and Recessiveness
Mendel’s experiments with pea plants suggested that: 1) two types of
“units” or alleles exist for every gene; 2) alleles maintain their integrity in
each generation (no blending); and 3) in the presence of the dominant allele,
the recessive allele is hidden, with no contribution to the phenotype.
Therefore, recessive alleles can be “carried” and not expressed by
individuals. Such heterozygous individuals are sometimes referred to as
“carriers.” Since then, genetic studies in other organisms have shown that
much more complexity exists, but that the fundamental principles of
Mendelian genetics still hold true. In the sections to follow, we consider
some of the extensions of Mendelism.
Incomplete Dominance
Mendel’s results, demonstrating that traits are inherited as dominant and
recessive pairs, contradicted the view at that time that offspring exhibited a
blend of their parents’ traits. However, the heterozygote phenotype
occasionally does appear to be intermediate between the two parents. For
example, in the snapdragon, Antirrhinum majus ({link]), a cross between a
homozygous parent with white flowers (C’C™) and a homozygous parent
with red flowers (CC®) will produce offspring with pink flowers (C®C).
(Note that different genotypic abbreviations are used for Mendelian
extensions to distinguish these patterns from simple dominance and
recessiveness.) This pattern of inheritance is described as incomplete
dominance, meaning that one of the alleles appears in the phenotype in the
heterozygote, but not to the exclusion of the other, which can also be seen.
The allele for red flowers is incompletely dominant over the allele for white
flowers. However, the results of a heterozygote self-cross can still be
predicted, just as with Mendelian dominant and recessive crosses. In this
case, the genotypic ratio would be 1 CRC:2 CRCW:1 CYC", and the
phenotypic ratio would be 1:2:1 for red:pink:white. The basis for the
intermediate color in the heterozygote is simply that the pigment produced
by the red allele (anthocyanin) is diluted in the heterozygote and therefore
appears pink because of the white background of the flower petals.
These pink flowers of a
heterozygote snapdragon
result from incomplete
dominance. (credit:
"storebukkebruse"/Flickr)
Codominance
A variation on incomplete dominance is codominance, in which both
alleles for the same characteristic are simultaneously expressed in the
heterozygote. An example of codominance occurs in the ABO blood groups
of humans. The A and B alleles are expressed in the form of A or B
molecules present on the surface of red blood cells. Homozygotes (I4I4 and
1°18) express either the A or the B phenotype, and heterozygotes (I“I°)
express both phenotypes equally. The /4/8 individual has blood type AB. In
a self-cross between heterozygotes expressing a codominant trait, the three
possible offspring genotypes are phenotypically distinct. However, the 1:2:1
genotypic ratio characteristic of a Mendelian monohybrid cross still applies
((link]).
Codominant Cross
Genotypes Genotype ratio
This Punnet square shows an AB/AB
blood type cross
Multiple Alleles
Mendel implied that only two alleles, one dominant and one recessive,
could exist for a given gene. We now know that this is an
oversimplification. Although individual humans (and all diploid organisms)
can only have two alleles for a given gene, multiple alleles may exist at the
population level, such that many combinations of two alleles are observed.
Note that when many alleles exist for the same gene, the convention is to
denote the most common phenotype or genotype in the natural population
as the wild type (often abbreviated “+”). All other phenotypes or genotypes
are considered variants (mutants) of this typical form, meaning they deviate
from the wild type. The variant may be recessive or dominant to the wild-
type allele.
An example of multiple alleles is the ABO blood-type system in humans. In
this case, there are three alleles circulating in the population. The J“ allele
codes for A molecules on the red blood cells, the I? allele codes for B
molecules on the surface of red blood cells, and the i allele codes for no
molecules on the red blood cells. In this case, the [4 and I? alleles are
codominant with each other and are both dominant over the i allele.
Although there are three alleles present in a population, each individual
only gets two of the alleles from their parents. This produces the genotypes
and phenotypes shown in [link]. Notice that instead of three genotypes,
there are six different genotypes when there are three alleles. The number of
possible phenotypes depends on the dominance relationships between the
three alleles.
Inheritance of the ABO Blood System in Humans
Inheritance of the ABO blood system in
humans is shown.
Note:
Evolution in Action
Multiple Alleles Confer Drug Resistance in the Malaria Parasite
Malaria is a parasitic disease in humans that is transmitted by infected
female mosquitoes, including Anopheles gambiae, and is characterized by
cyclic high fevers, chills, flu-like symptoms, and severe anemia.
Plasmodium falciparum and P. vivax are the most common causative
agents of malaria, and P. falciparum is the most deadly. When promptly
and correctly treated, P. falciparum malaria has a mortality rate of 0.1
percent. However, in some parts of the world, the parasite has evolved
resistance to commonly used malaria treatments, so the most effective
malarial treatments can vary by geographic region.
In Southeast Asia, Africa, and South America, P. falciparum has developed
resistance to the anti-malarial drugs chloroquine, mefloquine, and
sulfadoxine-pyrimethamine. P. falciparum, which is haploid during the life
stage in which it is infective to humans, has evolved multiple drug-resistant
mutant alleles of the dhps gene. Varying degrees of sulfadoxine resistance
are associated with each of these alleles. Being haploid, P. falciparum
needs only one drug-resistant allele to express this trait.
In Southeast Asia, different sulfadoxine-resistant alleles of the dhps gene
are localized to different geographic regions. This is a common
evolutionary phenomenon that comes about because drug-resistant mutants
arise in a population and interbreed with other P. falciparum isolates in
close proximity. Sulfadoxine-resistant parasites cause considerable human
hardship in regions in which this drug is widely used as an over-the-
counter malaria remedy. As is common with pathogens that multiply to
large numbers within an infection cycle, P. falciparum evolves relatively
rapidly (over a decade or so) in response to the selective pressure of
commonly used anti-malarial drugs. For this reason, scientists must
constantly work to develop new drugs or drug combinations to combat the
worldwide malaria burden. |{otmote!
Sumiti Vinayak et al., “Origin and Evolution of Sulfadoxine Resistant
Plasmodium falciparum,” PLoS Pathogens 6 (2010): e1000830.
Sex-Linked Traits
In humans, as well as in many other animals and some plants, the sex of the
individual is determined by sex chromosomes—one pair of non-
homologous chromosomes. Until now, we have only considered inheritance
patterns among non-sex chromosomes, or autosomes. In addition to 22
homologous pairs of autosomes, human females have a homologous pair of
X chromosomes, whereas human males have an XY chromosome pair.
Although the Y chromosome contains a small region of similarity to the X
chromosome so that they can pair during meiosis, the Y chromosome is
much shorter and contains fewer genes. When a gene being examined is
present on the X, but not the Y, chromosome, it is X-linked.
Eye color in Drosophila, the common fruit fly, was the first X-linked trait to
be identified. Thomas Hunt Morgan mapped this trait to the X chromosome
in 1910. Like humans, Drosophila males have an XY chromosome pair, and
females are XX. In flies the wild-type eye color is red (X”) and is dominant
to white eye color (X™) ([link]). Because of the location of the eye-color
gene, reciprocal crosses do not produce the same offspring ratios. Males are
said to be hemizygous, in that they have only one allele for any X-linked
characteristic. Hemizygosity makes descriptions of dominance and
recessiveness irrelevant for XY males. Drosophila males lack the white
gene on the Y chromosome; that is, their genotype can only be XWY or
XY. In contrast, females have two allele copies of this gene and can be
KOK XK Or KX,
In Drosophila, the gene for eye color
is located on the X chromosome. Red
eye color is wild-type and is dominant
to white eye color.
In an X-linked cross, the genotypes of F, and F, offspring depend on
whether the recessive trait was expressed by the male or the female in the P
generation. With respect to Drosophila eye color, when the P male
expresses the white-eye phenotype and the female is homozygously red-
eyed, all members of the F; generation exhibit red eyes ([link]). The F;
females are heterozygous (X“X”), and the males are all XY, having
received their X chromosome from the homozygous dominant P female and
their Y chromosome from the P male. A subsequent cross between the
XX” female and the X”Y male would produce only red-eyed females
(with X“X™ or X“X™ genotypes) and both red- and white-eyed males (with
XWY or X”Y genotypes). Now, consider a cross between a homozygous
white-eyed female and a male with red eyes. The F; generation would
exhibit only heterozygous red-eyed females (X“X”) and only white-eyed
males (X“Y). Half of the F, females would be red-eyed (XX) and half
would be white-eyed (X“X™). Similarly, half of the F, males would be red-
eyed (XY) and half would be white-eyed (X“Y).
Note:
Punnett Square Analysis of a Sex-linked Trait
All female offspring
have red eyes.
All male offspring
have white eyes.
Crosses involving sex-linked traits often
give rise to different phenotypes for the
different sexes of offspring, as is the case for
this cross involving red and white eye color
in Drosophila. In the diagram, w is the
white-eye mutant allele and W is the wild-
type, red-eye allele.
Discoveries in fruit fly genetics can be applied to human genetics. When a
female parent is homozygous for a recessive X-linked trait, she will pass the
trait on to 100 percent of her male offspring, because the males will receive
the Y chromosome from the male parent. In humans, the alleles for certain
conditions (some color-blindness, hemophilia, and muscular dystrophy) are
X-linked. Females who are heterozygous for these diseases are said to be
carriers and may not exhibit any phenotypic effects. These females will pass
the disease to half of their sons and will pass carrier status to half of their
daughters; therefore, X-linked traits appear more frequently in males than
females.
In some groups of organisms with sex chromosomes, the sex with the non-
homologous sex chromosomes is the female rather than the male. This is
the case for all birds. In this case, sex-linked traits will be more likely to
appear in the female, in whom they are hemizygous.
Linked Genes Violate the Law of Independent Assortment
Although all of Mendel’s pea plant characteristics behaved according to the
law of independent assortment, we now know that some allele combinations
are not inherited independently of each other. Genes that are located on
separate, non-homologous chromosomes will always sort independently.
However, each chromosome contains hundreds or thousands of genes,
organized linearly on chromosomes like beads on a string. The segregation
of alleles into gametes can be influenced by linkage, in which genes that
are located physically close to each other on the same chromosome are
more likely to be inherited as a pair. However, because of the process of
recombination, or “crossover,” it is possible for two genes on the same
chromosome to behave independently, or as if they are not linked. To
understand this, let us consider the biological basis of gene linkage and
recombination.
Homologous chromosomes possess the same genes in the same order,
though the specific alleles of the gene can be different on each of the two
chromosomes. Recall that during interphase and prophase I of meiosis,
homologous chromosomes first replicate and then synapse, with like genes
on the homologs aligning with each other. At this stage, segments of
homologous chromosomes exchange linear segments of genetic material
({link]). This process is called recombination, or crossover, and it is a
common genetic process. Because the genes are aligned during
recombination, the gene order is not altered. Instead, the result of
recombination is that maternal and paternal alleles are combined onto the
same chromosome. Across a given chromosome, several recombination
events may occur, causing extensive shuffling of alleles.
Homologous Chromosome Recombinant
chromosomes crossover chromosomes
aligned
Non-recombinant
chromosomes
The process of crossover, or recombination, occurs
when two homologous chromosomes align and
exchange a segment of genetic material.
When two genes are located on the same chromosome, they are considered
linked, and their alleles tend to be transmitted through meiosis together. To
exemplify this, imagine a dihybrid cross involving flower color and plant
height in which the genes are next to each other on the chromosome. If one
homologous chromosome has alleles for tall plants and red flowers, and the
other chromosome has genes for short plants and yellow flowers, then when
the gametes are formed, the tall and red alleles will tend to go together into
a gamete and the short and yellow alleles will go into other gametes. These
are called the parental genotypes because they have been inherited intact
from the parents of the individual producing gametes. But unlike if the
genes were on different chromosomes, there will be no gametes with tall
and yellow alleles and no gametes with short and red alleles. If you create a
Punnett square with these gametes, you will see that the classical Mendelian
prediction of a 9:3:3:1 outcome of a dihybrid cross would not apply. As the
distance between two genes increases, the probability of one or more
crossovers between them increases and the genes behave more like they are
on separate chromosomes. Geneticists have used the proportion of
recombinant gametes (the ones not like the parents) as a measure of how far
apart genes are on a chromosome. Using this information, they have
constructed linkage maps of genes on chromosomes for well-studied
organisms, including humans.
Mendel’s seminal publication makes no mention of linkage, and many
researchers have questioned whether he encountered linkage but chose not
to publish those crosses out of concern that they would invalidate his
independent assortment postulate. The garden pea has seven chromosomes,
and some have suggested that his choice of seven characteristics was not a
coincidence. However, even if the genes he examined were not located on
separate chromosomes, it is possible that he simply did not observe linkage
because of the extensive shuffling effects of recombination.
Population Evolution
Introduction
"Genetics is to biology what atomic theory is to physics. Its principle is
clear: that inheritance is based on particles and not on fluids. Instead of the
essence of each parent mixing, with each child the blend of those who made
him, information is passed on as a Series of units. The bodies of successive
generations transport them through time, so that a long-lost character may
emerge in a distant descendant. The genes themselves may be older than the
species that bear them." — John Stephen Jones, Almost Like a Whale: The
Origin of Species Updated. Doubleday, 1999.
The mechanisms of inheritance, or genetics, were not understood at the time
Charles Darwin and Alfred Russel Wallace were developing their idea of
natural selection. This lack of understanding was a stumbling block to
understanding many aspects of evolution. In fact, the predominant (and
incorrect) genetic theory of the time, blending inheritance, made it difficult
to understand how natural selection might operate. Darwin and Wallace
were unaware of the genetics work by Austrian monk Gregor Mendel,
which was published in 1866, not long after publication of Darwin's book,
On the Origin of Species. Mendel’s work was rediscovered in the early
twentieth century at which time geneticists were rapidly coming to an
understanding of the basics of inheritance. Initially, the newly discovered
particulate nature of genes made it difficult for biologists to understand how
gradual evolution could occur. But over the next few decades genetics and
evolution were integrated in what became known as the modern synthesis
—the coherent understanding of the relationship between natural selection
and genetics that took shape by the 1940s and is generally accepted today.
In sum, the modern synthesis describes how evolutionary processes, such as
natural selection, can affect a population’s genetic makeup, and, in turn,
how this can result in the gradual evolution of populations and species. The
theory also connects this change of a population over time, called
microevolution, with the processes that gave rise to new species and higher
taxonomic groups with widely divergent characters, called
macroevolution.
Note:
Evolution and Flu Vaccines
Every fall, the media starts reporting on flu vaccinations and potential
outbreaks. Scientists, health experts, and institutions determine
recommendations for different parts of the population, predict optimal
production and inoculation schedules, create vaccines, and set up clinics to
provide inoculations. You may think of the annual flu shot as a lot of media
hype, an important health protection, or just a briefly uncomfortable prick
in your arm. But do you think of it in terms of evolution?
The media hype of annual flu shots is scientifically grounded in our
understanding of evolution. Each year, scientists across the globe strive to
predict the flu strains that they anticipate being most widespread and
harmful in the coming year. This knowledge is based in how flu strains
have evolved over time and over the past few flu seasons. Scientists then
work to create the most effective vaccine to combat those selected strains.
Hundreds of millions of doses are produced in a short period in order to
provide vaccinations to key populations at the optimal time.
Because viruses, like the flu, evolve very quickly (especially in
evolutionary time), this poses quite a challenge. Viruses mutate and
replicate at a fast rate, so the vaccine developed to protect against last
year’s flu strain may not provide the protection needed against the coming
year’s strain. Evolution of these viruses means continued adaptions to
ensure survival, including adaptations to survive previous vaccines.
Population Genetics
Recall that a gene for a particular character may have several alleles, or
variants, that code for different traits associated with that character. For
example, in the ABO blood type system in humans, three alleles determine
the particular blood-type protein on the surface of red blood cells. Each
individual in a population of diploid organisms can only carry two alleles
for a particular gene, but more than two may be present in the individuals
that make up the population. Mendel followed alleles as they were inherited
from parent to offspring. In the early twentieth century, biologists in a field
of study known as population genetics began to study how selective forces
change a population through changes in allele and genotypic frequencies.
The allele frequency (or gene frequency) is the rate at which a specific
allele appears within a population. Until now we have discussed evolution
as a change in the characteristics of a population of organisms, but behind
that phenotypic change is genetic change. In population genetics, the term
evolution is defined as a change in the frequency of an allele in a
population. Using the ABO blood type system as an example, the frequency
of one of the alleles, I“, is the number of copies of that allele divided by all
the copies of the ABO gene in the population. For example, a study in
Jordan!2mote] found a frequency of I“ to be 26.1 percent. The I® and [°
alleles made up 13.4 percent and 60.5 percent of the alleles respectively,
and all of the frequencies added up to 100 percent. A change in this
frequency over time would constitute evolution in the population.
Sahar S. Hanania, Dhia S. Hassawi, and Nidal M. Irshaid, “Allele
Frequency and Molecular Genotypes of ABO Blood Group System in a
Jordanian Population,” Journal of Medical Sciences 7 (2007): 51-58,
doi: 10.3923/jms.2007.51.58.
The allele frequency within a given population can change depending on
environmental factors; therefore, certain alleles become more widespread
than others during the process of natural selection. Natural selection can
alter the population’s genetic makeup; for example, if a given allele confers
a phenotype that allows an individual to better survive or have more
offspring. Because many of those offspring will also carry the beneficial
allele, and often the corresponding phenotype, they will have more
offspring of their own that also carry the allele, thus, perpetuating the cycle.
Over time, the allele will spread throughout the population. Some alleles
will quickly become fixed in this way, meaning that every individual of the
population will carry the allele, while detrimental mutations may be swiftly
eliminated if derived from a dominant allele from the gene pool. The gene
pool is the sum of all the alleles in a population.
Sometimes, allele frequencies within a population change randomly with no
advantage to the population over existing allele frequencies. This
phenomenon is called genetic drift. Natural selection and genetic drift
usually occur simultaneously in populations and are not isolated events. It is
hard to determine which process dominates because it is often nearly
impossible to determine the cause of change in allele frequencies at each
occurrence. An event that initiates an allele frequency change in an isolated
part of the population, which is not typical of the original population, is
called the founder effect. Natural selection, random drift, and founder
effects can lead to significant changes in the genome of a population.
Hardy-Weinberg Principle of Equilibrium
In the early twentieth century, English mathematician Godfrey Hardy and
German physician Wilhelm Weinberg stated the principle of equilibrium to
describe the genetic makeup of a population. The theory, which later
became known as the Hardy-Weinberg principle of equilibrium, states
that a population’s allele and genotype frequencies are inherently stable—
unless some kind of evolutionary force is acting upon the population,
neither the allele nor the genotypic frequencies would change. The Hardy-
Weinberg principle assumes conditions with no mutations, migration,
emigration, or selective pressure for or against genotype, plus an infinite
population; while no population can satisfy those conditions, the principle
offers a useful model against which to compare real population changes.
Working under this theory, population geneticists represent different alleles
as different variables in their mathematical models. The variable p, for
example, often represents the frequency of a particular allele, say Y for the
trait of yellow in Mendel’s peas, while the variable q represents the
frequency of y alleles that confer the color green. If these are the only two
possible alleles for a given locus in the population, p + gq = 1. In other
words, all the p alleles and all the g alleles make up all of the alleles for that
locus that are found in the population.
But what ultimately interests most biologists is not the frequencies of
different alleles, but the frequencies of the resulting genotypes, known as
the population’s genetic structure, from which scientists can surmise the
distribution of phenotypes. If the phenotype is observed, only the genotype
of the homozygous recessive alleles can be known; the calculations provide
an estimate of the remaining genotypes. Since each individual carries two
alleles per gene, if the allele frequencies (p and q) are known, predicting the
frequencies of these genotypes is a simple mathematical calculation to
determine the probability of getting these genotypes if two alleles are drawn
at random from the gene pool. So in the above scenario, an individual pea
plant could be pp (YY), and thus produce yellow peas; pq (Yy), also
yellow; or qq (yy), and thus producing green peas ([link]). In other words,
the frequency of pp individuals is simply p?; the frequency of pq
individuals is 2pq; and the frequency of qq individuals is q?. And, again, if
p and q are the only two possible alleles for a given trait in the population,
these genotypes frequencies will sum to one: p* + 2pq + q? = 1.
Note:
Hardy-Weinberg Principle
Parent generation
Phenotype
Genotypic frequency
Number of individuals
(total = 500)
Number of alleles Y: 490 + 210 = 700
in gene pool
(total = 1000) gy
TALON 300 y
Allelic frequency 1000 total ~~
7=p 7000 total — “2-9
Hardy-Weinberg p (.7) q (.3)
analysis
2(.7)(.3)
8
Predicted Predicted Predicted
frequency frequency frequency
of YY of Yy of yy
offspring offspring offspring
When populations are in the Hardy-Weinberg
equilibrium, the allelic frequency is stable from
generation to generation and the distribution of
alleles can be determined from the Hardy-
Weinberg equation. If the allelic frequency
measured in the field differs from the predicted
value, scientists can make inferences about what
evolutionary forces are at play.
In theory, if a population is at equilibrium—that is, there are no
evolutionary forces acting upon it—generation after generation would have
the same gene pool and genetic structure, and these equations would all
hold true all of the time. Of course, even Hardy and Weinberg recognized
that no natural population is immune to evolution. Populations in nature are
constantly changing in genetic makeup due to drift, mutation, possibly
migration, and selection. As a result, the only way to determine the exact
distribution of phenotypes in a population is to go out and count them. But
the Hardy-Weinberg principle gives scientists a mathematical baseline of a
non-evolving population to which they can compare evolving populations
and thereby infer what evolutionary forces might be at play. If the
frequencies of alleles or genotypes deviate from the value expected from
the Hardy-Weinberg equation, then the population is evolving.
Population Genetics
Introduction
" The proof given by Wright, that non-adaptive differentiation will occur in
small populations owing to ‘drift’, or the chance fixation of some new
mutation or recombination, is one of the most important results of
mathematical analysis applied to the facts of neo-mendelism. It gives
accident as well as adaptation a place in evolution, and at one stroke
explains many facts which puzzled earlier selectionists, notably the much
greater degree of divergence shown by island than mainland forms, by
forms in isolated lakes than in continuous river-systems. " Sir Julian
Huxley, 1942
The leap from understanding genes and mutations to an understanding of
the evolution of populations required the identification of other mechanisms
that allowed genes to become common or uncommon in populations.
Individuals of a population often display different phenotypes, or express
different alleles of a particular gene, referred to as polymorphisms.
Populations with two or more variations of particular characteristics are
called polymorphic. The distribution of phenotypes among individuals,
known as the population variation, is influenced by a number of factors,
including the population’s genetic structure and the environment ((link]).
Understanding the sources of a phenotypic variation in a population is
important for determining how a population will evolve in response to
different evolutionary pressures.
The distribution of phenotypes in this
litter of kittens illustrates population
variation. (credit: Pieter Lanser)
Genetic Variance
Natural selection and some of the other evolutionary forces can only act on
heritable traits, namely an organism’s genetic code. Because alleles are
passed from parent to offspring, those that confer beneficial traits or
behaviors may be selected for, while deleterious alleles may be selected
against. Acquired traits, for the most part, are not heritable. For example, if
an athlete works out in the gym every day, building up muscle strength, the
athlete’s offspring will not necessarily grow up to be a body builder. If there
is a genetic basis for the ability to run fast, on the other hand, this may be
passed to a child.
Heritability is the fraction of phenotype variation that can be attributed to
genetic differences, or genetic variance, among individuals in a population.
The greater the hereditability of a population’s phenotypic variation, the
more susceptible it is to the evolutionary forces that act on heritable
variation.
The diversity of alleles and genotypes within a population is called genetic
variance. When scientists are involved in the breeding of a species, such as
with animals in zoos and nature preserves, they try to increase a
population’s genetic variance to preserve as much of the phenotypic
diversity as they can. This also helps reduce the risks associated with
inbreeding, the mating of closely related individuals, which can have the
undesirable effect of bringing together deleterious recessive mutations that
can cause abnormalities and susceptibility to disease. For example, a
disease that is caused by a rare, recessive allele might exist in a population,
but it will only manifest itself when an individual carries two copies of the
allele. Because the allele is rare in a normal, healthy population with
unrestricted habitat, the chance that two carriers will mate is low, and even
then, only 25 percent of their offspring will inherit the disease allele from
both parents. While it is likely to happen at some point, it will not happen
frequently enough for natural selection to be able to swiftly eliminate the
allele from the population, and as a result, the allele will be maintained at
low levels in the gene pool. However, if a family of carriers begins to
interbreed with each other, this will dramatically increase the likelihood of
two carriers mating and eventually producing diseased offspring, a
phenomenon known as inbreeding depression.
Changes in allele frequencies that are identified in a population can shed
light on how it is evolving. In addition to natural selection, there are other
evolutionary forces that could be in play: natural selection, genetic drift,
gene flow, mutation, and nonrandom mating.
Natural Selection
The theory of natural selection stems from the observation that some
individuals in a population are more likely to survive longer and have more
offspring than others; thus, they will pass on more of their genes to the next
generation. A big, powerful male gorilla, for example, is much more likely
than a smaller, weaker one to become the population’s silverback, the
pack’s leader who mates far more than the other males of the group. The
pack leader will father more offspring, who share half of his genes, and are
likely to also grow bigger and stronger like their father. Over time, the
genes for bigger size will increase in frequency in the population, and the
population will, as a result, grow larger on average. That is, this would
occur if this particular selection pressure, or driving selective force, were
the only one acting on the population. In other examples, better camouflage
or a stronger resistance to drought might pose a selection pressure.
Genetic Drift
Another way a population’s allele and genotype frequencies can change is
genetic drift ({link]), which is simply the effect of chance. By chance,
some individuals will have more offspring than others—not due to an
advantage conferred by some genetically-encoded trait, but just because one
male happened to be in the right place at the right time (when the receptive
female walked by) or because the other one happened to be in the wrong
place at the wrong time (when a fox was hunting).
Note:
First generation
p (B allele frequency) = .5
p (B allele frequency) =.5
5 rabbits reproduce
Second generation
p (B allele frequency) = .7
p (B allele frequency) = .3
dddd.
G0. 0. a. @.
2 rabbits reproduce |
Third generation
p (B allele frequency) =1
p (B allele frequency) =0
@.¢.@.¢. @.
@.d.¢. ¢. @.
Genetic drift in a population
can lead to the elimination of
an allele from a population
by chance. In this example,
rabbits with the brown coat
color allele (B) are dominant
over rabbits with the white
coat color allele (b). In the
first generation, the two
alleles occur with equal
frequency in the population,
resulting in p and q values of
.o. Only half of the
individuals reproduce,
resulting in a second
generation with p and q
values of .7 and .3,
respectively. Only two
individuals in the second
generation reproduce, and by
chance these individuals are
homozygous dominant for
brown coat color. As a result,
in the third generation the
recessive b allele is lost.
Small populations are more susceptible to the forces of genetic drift. Large
populations, on the other hand, are buffered against the effects of chance. If
one individual of a population of 10 individuals happens to die at a young
age before it leaves any offspring to the next generation, all of its genes—
1/10 of the population’s gene pool—will be suddenly lost. In a population
of 100, that’s only 1 percent of the overall gene pool; therefore, it is much
less impactful on the population’s genetic structure.
Genetic drift can also be magnified by natural events, such as a natural
disaster that kills—at random—a large portion of the population. Known as
the bottleneck effect, it results in a large portion of the genome suddenly
being wiped out ({link]). In one fell swoop, the genetic structure of the
survivors becomes the genetic structure of the entire population, which may
be very different from the pre-disaster population.
Original
population
Bottlenecking
event
Surviving
population
A chance event or catastrophe
can reduce the genetic
variability within a population.
Another scenario in which populations might experience a strong influence
of genetic drift is if some portion of the population leaves to start a new
population in a new location or if a population gets divided by a physical
barrier of some kind. In this situation, those individuals are unlikely to be
representative of the entire population, which results in the founder effect.
The founder effect occurs when the genetic structure changes to match that
of the new population’s founding fathers and mothers. The founder effect is
believed to have been a key factor in the genetic history of the Afrikaner
population of Dutch settlers in South Africa, as evidenced by mutations that
are common in Afrikaners but rare in most other populations. This is likely
due to the fact that a higher-than-normal proportion of the founding
colonists carried these mutations. As a result, the population expresses
unusually high incidences of Huntington’s disease (HD) and Fanconi
anemia (FA), a genetic disorder known to cause blood marrow and
congenital abnormalities—even cancer, omote!
A. J. Tipping et al., “Molecular and Genealogical Evidence for a Founder
Effect in Fanconi Anemia Families of the Afrikaner Population of South
Africa,” PNAS 98, no. 10 (2001): 5734-5739, doi:
10.1073/pnas.091402398.
Gene Flow
Another important evolutionary force is gene flow: the flow of alleles in
and out of a population due to the migration of individuals or gametes
({link]). While some populations are fairly stable, others experience more
flux. Many plants, for example, send their pollen far and wide, by wind or
by bird, to pollinate other populations of the same species some distance
away. Even a population that may initially appear to be stable, such as a
pride of lions, can experience its fair share of immigration and emigration
as developing males leave their mothers to seek out a new pride with
genetically unrelated females. This variable flow of individuals in and out
of the group not only changes the gene structure of the population, but it
can also introduce new genetic variation to populations in different
geological locations and habitats.
ve.
ae
Gene flow can occur when an individual
travels from one geographic location to
another.
Mutation
Mutations are changes to an organism’s DNA and are an important driver of
diversity in populations. Species evolve because of the accumulation of
mutations that occur over time. The appearance of new mutations is the
most common way to introduce novel genotypic and phenotypic variance.
Some mutations are unfavorable or harmful and are quickly eliminated
from the population by natural selection. Others are beneficial and will
spread through the population. Whether or not a mutation is beneficial or
harmful is determined by whether it helps an organism survive to sexual
maturity and reproduce. Some mutations do not do anything and can linger,
unaffected by natural selection, in the genome. Some can have a dramatic
effect on a gene and the resulting phenotype.
Nonrandom Mating
If individuals nonrandomly mate with their peers, the result can be a
changing population. There are many reasons nonrandom mating occurs.
One reason is mate choice; for example, female peahens may prefer
peacocks with bigger, brighter tails. Traits that lead to more matings for an
individual become selected for by natural selection. One common form of
mate choice, called assortative mating, is an individual’s preference to mate
with partners who are phenotypically similar to themselves.
Another cause of nonrandom mating is physical location. This is especially
true in large populations spread over large geographic distances where not
all individuals will have equal access to one another. Some might be miles
apart through woods or over rough terrain, while others might live
immediately nearby.
Formation of New Species
Introduction
" As buds give rise by growth to fresh buds, and these, if vigorous, branch
out and overtop on all sides many a feebler branch, so by generation I
believe it has been with the great Tree of Life, which fills with its dead and
broken branches the crust of the earth, and covers the surface with its ever
branching and beautiful ramifications. " Charles Darwin, On the Origin of
Species by Means of Natural Selection; or, The Preservation of Favoured
Races in the Struggle for Life, 1859
Darwin's insight about the branching tree of life is the easiest way to think
about the origin of species. The twigs at the ends of branches may be
different, but they all are connected and related. Although all life on earth
shares various genetic similarities, only certain organisms combine genetic
information by sexual reproduction and have offspring that can then
successfully reproduce. Scientists call such organisms members of the same
biological species.
Species and the Ability to Reproduce
A species is a group of individual organisms that interbreed and produce
fertile, viable offspring. According to this definition, one species is
distinguished from another when, in nature, it is not possible for matings
between individuals from each species to produce fertile offspring. This
idea of a species is called the biological species concept and is one of the
most widely accepted species concepts.
Members of the same species share both external and internal
characteristics, which develop from their DNA. The closer relationship two
organisms share, the more DNA they have in common, just like people and
their families. Your DNA is likely to be more like your father or mother’s
DNA than your cousin or grandparent’s DNA. Organisms of the same
species have the highest level of DNA alignment and therefore share
characteristics and behaviors that lead to successful reproduction.
Species’ appearance can be misleading in suggesting an ability or inability
to mate. For example, even though domestic dogs (Canis lupus familiaris)
display phenotypic differences, such as size, build, and coat, most dogs can
interbreed and produce viable puppies that can mature and sexually
reproduce ([link]).
The (a) poodle and (b) cocker spaniel can reproduce to
produce a breed known as (c) the cockapoo. (credit a:
modification of work by Sally Eller, Tom Reese; credit
b: modification of work by Jeremy McWilliams; credit
c: modification of work by Kathleen Conklin)
In other cases, individuals may appear similar although they are not
members of the same species. For example, even though bald eagles
(Haliaeetus leucocephalus) and African fish eagles (Haliaeetus vocifer) are
both birds and eagles, each belongs to a separate species group ([link]). If
humans were to artificially intervene and fertilize the egg of a bald eagle
with the sperm of an African fish eagle and a chick did hatch, that offspring,
called a hybrid (a cross between two species), would probably be infertile
—unable to successfully reproduce after it reached maturity. Different
species may have different genes that are active in development; therefore,
it may not be possible to develop a viable offspring with two different sets
of directions. Thus, even though hybridization may take place, the two
species still remain separate.
The (a) African fish eagle is similar in
appearance to the (b) bald eagle, but the two
birds are members of different species.
(credit a: modification of work by Nigel
Wedge; credit b: modification of work by
U.S. Fish and Wildlife Service)
Populations of species share a gene pool: a collection of all the variants of
genes in the species. Again, the basis to any changes in a group or
population of organisms must be genetic for this is the only way to share
and pass on traits. When variations occur within a species, they can only be
passed to the next generation along two main pathways: asexual
reproduction or sexual reproduction. The change will be passed on
asexually simply if the reproducing cell possesses the changed trait. For the
changed trait to be passed on by sexual reproduction, a gamete, such as a
sperm or egg cell, must possess the changed trait. In other words, sexually-
reproducing organisms can experience several genetic changes in their body
cells, but if these changes do not occur in a sperm or egg cell, the changed
trait will never reach the next generation. Only heritable traits can evolve.
Therefore, reproduction plays a paramount role for genetic change to take
root in a population or species. In short, organisms must be able to
reproduce with each other to pass new traits to offspring.
Speciation
The biological definition of species, which works for sexually reproducing
organisms, is a group of actually or potentially interbreeding individuals.
There are exceptions to this rule. Many species are similar enough that
hybrid offspring are possible and may often occur in nature, but for the
majority of species this rule generally holds. In fact, the presence in nature
of hybrids between similar species suggests that they may have descended
from a single interbreeding species, and the speciation process may not yet
be completed.
Given the extraordinary diversity of life on the planet there must be
mechanisms for speciation: the formation of two species from one original
species. Darwin envisioned this process as a branching event and
diagrammed the process in the only illustration found in On the Origin of
Species ([{link]a). Compare this illustration to the diagram of elephant
evolution ([link]b), which shows that as one species changes over time, it
branches to form more than one new species, repeatedly, as long as the
population survives or until the organism becomes extinct.
Elephas
) es : 2 Pipi lee <p pa ee ESS =f2p, Loxodonta
Se ‘a aoe Gn: =“ ania 7+ ™Y | (asian elephant) [
_,, (African elephant)
Mammuthus
(mammoth)
Mammut Stegodon
(mastodon)
(a) (b)
The only illustration in Darwin's On the Origin of Species is (a) a
diagram showing speciation events leading to biological diversity. The
diagram shows similarities to phylogenetic charts that are drawn today
to illustrate the relationships of species. (b) Modern elephants evolved
from the Palaeomastodon, a species that lived in Egypt 35-50 million
years ago.
For speciation to occur, two new populations must be formed from one
original population and they must evolve in such a way that it becomes
impossible for individuals from the two new populations to interbreed.
Biologists have proposed mechanisms by which this could occur that fall
into two broad categories. Allopatric speciation (allo- = "other"; -patric =
"homeland") involves geographic separation of populations from a parent
species and subsequent evolution. Sympatric speciation (sym- = "same"; -
patric = "homeland") involves speciation occurring within a parent species
remaining in one location.
Biologists think of speciation events as the splitting of one ancestral species
into two descendant species. There is no reason why there might not be
more than two species formed at one time except that it is less likely and
multiple events can be conceptualized as single splits occurring close in
time.
Allopatric Speciation
A geographically continuous population has a gene pool that is relatively
homogeneous. Gene flow, the movement of alleles across the range of the
species, is relatively free because individuals can move and then mate with
individuals in their new location. Thus, the frequency of an allele at one end
of a distribution will be similar to the frequency of the allele at the other
end. When populations become geographically discontinuous, that free-
flow of alleles is prevented. When that separation lasts for a period of time,
the two populations are able to evolve along different trajectories. Thus,
their allele frequencies at numerous genetic loci gradually become more
and more different as new alleles independently arise by mutation in each
population. Typically, environmental conditions, such as climate, resources,
predators, and competitors for the two populations will differ causing
natural selection to favor divergent adaptations in each group.
Isolation of populations leading to allopatric speciation can occur in a
variety of ways: a river forming a new branch, erosion forming a new
valley, a group of organisms traveling to a new location without the ability
to return, or seeds floating over the ocean to an island. The nature of the
geographic separation necessary to isolate populations depends entirely on
the biology of the organism and its potential for dispersal. If two flying
insect populations took up residence in separate nearby valleys, chances
are, individuals from each population would fly back and forth continuing
gene flow. However, if two rodent populations became divided by the
formation of a new lake, continued gene flow would be unlikely; therefore,
speciation would be more likely.
Biologists group allopatric processes into two categories: dispersal and
vicariance. Dispersal is when a few members of a species move to a new
geographical area, and vicariance is when a natural situation arises to
physically divide organisms.
Scientists have documented numerous cases of allopatric speciation taking
place. For example, along the west coast of the United States, two separate
sub-species of spotted owls exist. The northern spotted owl has genetic and
phenotypic differences from its close relative: the Mexican spotted owl,
which lives in the south ([Link]).
Mexican Spotted Owl
The northern spotted owl and
the Mexican spotted owl
inhabit geographically
separate locations with
different climates and
ecosystems. The owl is an
example of allopatric
speciation. (credit "northern
spotted owl": modification of
work by John and Karen
Hollingsworth; credit
"Mexican spotted owl":
modification of work by Bill
Radke)
Additionally, scientists have found that the further the distance between two
groups that once were the same species, the more likely it is that speciation
will occur. This seems logical because as the distance increases, the various
environmental factors would likely have less in common than locations in
close proximity. Consider the two owls: in the north, the climate is cooler
than in the south; the types of organisms in each ecosystem differ, as do
their behaviors and habits; also, the hunting habits and prey choices of the
southern owls vary from the northern owls. These variances can lead to
evolved differences in the owls, and speciation likely will occur.
Adaptive Radiation
In some cases, a population of one species disperses throughout an area,
and each finds a distinct niche or isolated habitat. Over time, the varied
demands of their new lifestyles lead to multiple speciation events
originating from a single species. This is called adaptive radiation because
many adaptations evolve from a single point of origin; thus, causing the
species to radiate into several new ones. Island archipelagos like the
Hawaiian Islands provide an ideal context for adaptive radiation events
because water surrounds each island which leads to geographical isolation
for many organisms. The Hawaiian honeycreeper illustrates one example of
adaptive radiation. From a single species, called the founder species,
numerous species have evolved, including the six shown in [link].
The honeycreeper birds illustrate adaptive
radiation. From one original species of
bird, multiple others evolved, each with
its own distinctive characteristics.
Notice the differences in the species’ beaks in [link]. Evolution in response
to natural selection based on specific food sources in each new habitat led
to evolution of a different beak suited to the specific food source. The seed-
eating bird has a thicker, stronger beak which is suited to break hard nuts.
The nectar-eating birds have long beaks to dip into flowers to reach the
nectar. The insect-eating birds have beaks like swords, appropriate for
stabbing and impaling insects. Darwin’s finches are another example of
adaptive radiation in an archipelago.
Sympatric Speciation
Can divergence occur if no physical barriers are in place to separate
individuals who continue to live and reproduce in the same habitat? The
answer is yes. The process of speciation within the same space is called
sympatric speciation; the prefix “sym” means same, so “sympatric” means
“same homeland” in contrast to “allopatric” meaning “other homeland.” A
number of mechanisms for sympatric speciation have been proposed and
studied.
One form of sympatric speciation can begin with a serious chromosomal
error during cell division. In a normal cell division event chromosomes
replicate, pair up, and then separate so that each new cell has the same
number of chromosomes. However, sometimes the pairs separate and the
end cell product has too many or too few individual chromosomes in a
condition called aneuploidy ([link]).
Note:
Aneuploidy Resulting in Offspring with 2n + 1 or 2n - 1 Chromosomes
Nondisjunction Mating with
during meiosis normal gamete
2n
eo -&
=
Oo e+
Diploid (2n)
Aneuploidy results when the gametes have too
many or too few chromosomes due to
nondisjunction during meiosis. In the example
shown here, the resulting offspring will have
2n+1 or 2n-1 chromosomes
Polyploidy is a condition in which a cell or organism has an extra set, or
sets, of chromosomes. Scientists have identified two main types of
polyploidy that can lead to reproductive isolation of an individual in the
polyploidy state. Reproductive isolation is the inability to interbreed. In
some cases, a polyploid individual will have two or more complete sets of
chromosomes from its own species in a condition called autopolyploidy
({link]). The prefix “auto-” means “self,” so the term means multiple
chromosomes from one’s own species. Polyploidy results from an error in
meiosis in which all of the chromosomes move into one cell instead of
separating.
of Chromosomes
—
Diploid parent (2n) Polyploid offspring (4n)
Autopolyploidy Resulting in Offspring with Two Sets
Autopolyploidy results when
mitosis is not followed by
cytokinesis.
For example, if a plant species with 2n = 6 produces autopolyploid gametes
that are also diploid (2n = 6, when they should be n = 3), the gametes now
have twice as many chromosomes as they should have. These new gametes
will be incompatible with the normal gametes produced by this plant
species. However, they could either self-pollinate or reproduce with other
autopolyploid plants with gametes having the same diploid number. In this
way, sympatric speciation can occur quickly by forming offspring with 4n
called a tetraploid. These individuals would immediately be able to
reproduce only with those of this new kind and not those of the ancestral
species.
The other form of polyploidy occurs when individuals of two different
species reproduce to form a viable offspring called an allopolyploid. The
prefix “allo-” means “other” (recall from allopatric): therefore, an
allopolyploid occurs when gametes from two different species combine.
[link] illustrates one possible way an allopolyploid can form. Notice how it
takes two generations, or two reproductive acts, before the viable fertile
hybrid results.
Alloploidy Resulting from Viable Matings between Two Species
Normal gamete
Oy 4 Polyploid
First gamete Second
Species 1 mating mating
4s
/ \he
Species 2 Polyploid gamete Normal gamete
Alloploidy results when two species mate to
produce viable offspring. In the example shown, a
normal gamete from one species fuses with a
polyploidy gamete from another. Two matings are
necessary to produce viable offspring.
The cultivated forms of wheat, cotton, and tobacco plants are all
allopolyploids. Although polyploidy occurs occasionally in animals, it takes
place most commonly in plants. (Animals with any of the types of
chromosomal aberrations described here are unlikely to survive and
produce normal offspring.) Scientists have discovered more than half of all
plant species studied relate back to a species evolved through polyploidy.
With such a high rate of polyploidy in plants, some scientists hypothesize
that this mechanism takes place more as an adaptation than as an error.
Reproductive Isolation
Given enough time, the genetic and phenotypic divergence between
populations will affect characters that influence reproduction: if individuals
of the two populations were to be brought together, mating would be less
likely, but if mating occurred, offspring would be non-viable or infertile.
Many types of diverging characters may affect the reproductive isolation,
the ability to interbreed, of the two populations.
Reproductive isolation can take place in a variety of ways. Scientists
organize them into two groups: prezygotic barriers and postzygotic barriers.
Recall that a zygote is a fertilized egg: the first cell of the development of
an organism that reproduces sexually. Therefore, a prezygotic barrier is a
mechanism that blocks reproduction or prevents fertilization when
organisms attempt reproduction. A postzygotic barrier occurs after
fertilization; this includes organisms that don’t survive the embryonic stage
and those that are born sterile.
Some types of prezygotic barriers prevent reproduction entirely. Many
organisms only reproduce at certain times of the year, often just annually.
Differences in breeding schedules, called temporal isolation, can act as a
form of reproductive isolation. For example, two species of frogs inhabit
the same area, but one reproduces from January to March, whereas the
other reproduces from March to May ((link]).
(a) (b)
These two related frog species exhibit temporal
reproductive isolation. (a) Rana aurora breeds
earlier in the year than (b) Rana boylii. (credit
a: modification of work by Mark R. Jennings,
USFWS; credit b: modification of work by
Alessandro Catenazzi)
In some cases, populations of a species move or are moved to a new habitat
and take up residence in a place that no longer overlaps with the other
populations of the same species. This situation is called habitat isolation.
Reproduction with the parent species ceases, and a new group exists that is
now reproductively and genetically independent. For example, a cricket
population that was divided after a flood could no longer interact with each
other. Over time, the forces of natural selection, mutation, and genetic drift
will likely result in the divergence of the two groups ([link]).
(a) Gryllus pennsylvanicus prefers (b) Gryllus firmus prefers loamy soil.
sandy soil.
Speciation can occur when two populations
occupy different habitats. The habitats need
not be far apart. The cricket (a) Gryllus
pennsylvanicus prefers sandy soil, and the
cricket (b) Gryllus firmus prefers loamy soil.
The two species can live in close proximity,
but because of their different soil
preferences, they became genetically
isolated.
Behavioral isolation occurs when the presence or absence of a specific
behavior prevents reproduction from taking place. For example, male
fireflies use specific light patterns to attract females. Various species of
fireflies display their lights differently. If a male of one species tried to
attract the female of another, she would not recognize the light pattern and
would not mate with the male.
Other prezygotic barriers work when differences in their gamete cells (eggs
and sperm) prevent fertilization from taking place; this is called a gametic
barrier. Similarly, in some cases closely related organisms try to mate, but
their reproductive structures simply do not fit together. For example,
damselfly males of different species have differently shaped reproductive
organs. If one species tries to mate with the female of another, their body
parts simply do not fit together. ((link]).
GS & ame
The shape of the male reproductive organ varies
among male damselfly species, and is only compatible
with the female of that species. Reproductive organ
incompatibility keeps the species reproductively
isolated.
In plants, certain structures aimed to attract one type of pollinator
simultaneously prevent a different pollinator from accessing the pollen. The
tunnel through which an animal must access nectar can vary widely in
length and diameter, which prevents the plant from being cross-pollinated
with a different species ((link]).
(a) Honeybee drinking nectar (b) Ruby-throated hummingbird drinking nectar from a
from a foxglove flower trumpet creeper flower
Some flowers have evolved to attract certain
pollinators. The (a) wide foxglove flower is
adapted for pollination by bees, while the (b)
long, tube-shaped trumpet creeper flower is
adapted for pollination by humming birds.
When fertilization takes place and a zygote forms, postzygotic barriers can
prevent reproduction. Hybrid individuals in many cases cannot form
normally in the womb and simply do not survive past the embryonic stages.
This is called hybrid inviability because the hybrid organisms simply are
not viable. In another postzygotic situation, reproduction leads to the birth
and growth of a hybrid that is sterile and unable to reproduce offspring of
their own; this is called hybrid sterility.
Habitat Influence on Speciation
Sympatric speciation may also take place in ways other than polyploidy.
For example, consider a species of fish that lives in a lake. As the
population grows, competition for food also grows. Under pressure to find
food, suppose that a group of these fish had the genetic flexibility to
discover and feed off another resource that was unused by the other fish.
What if this new food source was found at a different depth of the lake?
Over time, those feeding on the second food source would interact more
with each other than the other fish; therefore, they would breed together as
well. Offspring of these fish would likely behave as their parents: feeding
and living in the same area and keeping separate from the original
population. If this group of fish continued to remain separate from the first
population, eventually sympatric speciation might occur as more genetic
differences accumulated between them.
This scenario does play out in nature, as do others that lead to reproductive
isolation. One such place is Lake Victoria in Africa, famous for its
sympatric speciation of cichlid fish. Researchers have found hundreds of
sympatric speciation events in these fish, which have not only happened in
great number, but also over a short period of time. [link] shows this type of
speciation among a cichlid fish population in Nicaragua. In this locale, two
types of cichlids live in the same geographic location but have come to have
different morphologies that allow them to eat various food sources.
ABS
Thin-lipped cichlid Thick-lipped cichlid
Cichlid fish from Lake Apoyeque, Nicaragua, show evidence
of sympatric speciation. Lake Apoyeque, a crater lake, is 1800
years old, but genetic evidence indicates that the lake was
populated only 100 years ago by a single population of cichlid
fish. Nevertheless, two populations with distinct morphologies
and diets now exist in the lake, and scientists believe these
populations may be in an early stage of speciation.
Energy and Metabolism
Introduction
" [In research on bacteria metabolism] we have indeed much the same
position as an observer trying to gain an idea of the life of a household by
careful scrutiny of the persons and material arriving or leaving the house;
we keep accurate records of the foods and commodities left at the door and
patiently examine the contents of the dust-bin and endeavour to deduce
from such data the events occurring within the closed doors. " Marjory
Stephenson (1930)
Metabolism is indeed most closely studied by marking what goes in and
what comes out, both in terms of materials and energy. Scientists use the
term bioenergetics to discuss the concept of energy flow ([link]) through
living systems from ecosystems to cells. Cellular processes such as the
building and breaking down of complex molecules occur through stepwise
chemical reactions. Some of these chemical reactions are spontaneous and
release energy, whereas others require energy to proceed. Just as living
things must continually consume food to replenish what has been used,
cells must continually produce more energy to replenish that used by the
many energy-requiring chemical reactions that constantly take place. All of
the chemical reactions that take place inside cells, including those that use
energy and those that release energy, are the cell’s metabolism.
%
Most life forms on earth get their energy from the sun. Various
metabolic processes harvest and harness this energy which ultimately
leaves the system as heat (24 Law of Thermodynamics). The dashed
lines represent energy and the solid lines represent nutrients. (Image by
Eva Horne and Robert Bear)
Metabolism of Carbohydrates
The metabolism of sugar (a simple carbohydrate) is a classic example of the
many cellular processes that use and produce energy. Living things
consume sugar as a major energy source, because sugar molecules have a
great deal of energy stored within their bonds. The breakdown of glucose, a
simple sugar, is described by the equation:
Equation:
CgH20¢ “re 605 — 6CO, ae 6H,O + energy
Carbohydrates that are consumed have their origins in photosynthesizing
organisms like plants ((link]). During photosynthesis, plants use the energy
of sunlight to convert carbon dioxide gas (CO>) into sugar molecules, like
glucose (CgH,20¢). Because this process involves synthesizing a larger,
energy-storing molecule, it requires an input of energy to proceed. The
synthesis of glucose is described by this equation (notice that it is the
reverse of the previous equation):
Equation:
6CO, a 6H,O + energy —> CgH20¢ a 60,
During the chemical reactions of photosynthesis, energy is provided in the
form of a very high-energy molecule called ATP, or adenosine triphosphate,
which is the primary energy currency of all cells. Just as the dollar is used
as Currency to buy goods, cells use molecules of ATP as energy currency to
perform immediate work. The sugar (glucose) is stored as starch or
glycogen. Energy-storing polymers like these are broken down into glucose
to supply molecules of ATP.
Solar energy is required to synthesize a molecule of glucose during the
reactions of photosynthesis. In photosynthesis, light energy from the sun is
initially transformed into chemical energy that is temporally stored in the
energy carrier molecules ATP and NADPH (nicotinamide adenine
dinucleotide phosphate). The stored energy in ATP and NADPH is then
used later in photosynthesis to build one molecule of glucose from six
molecules of CO». This process is analogous to eating breakfast in the
morning to acquire energy for your body that can be used later in the day.
Under ideal conditions, energy from 18 molecules of ATP is required to
synthesize one molecule of glucose during the reactions of photosynthesis.
Glucose molecules can also be combined with and converted into other
types of sugars. When sugars are consumed, molecules of glucose
eventually make their way into each living cell of the organism. Inside the
cell, each sugar molecule is broken down through a complex series of
chemical reactions. The goal of these reactions is to harvest the energy
stored inside the sugar molecules. The harvested energy is used to make
high-energy ATP molecules, which can be used to perform work, powering
many chemical reactions in the cell. The amount of energy needed to make
one molecule of glucose from six molecules of carbon dioxide is 18
molecules of ATP and 12 molecules of NADPH (each one of which is
energetically equivalent to three molecules of ATP), or a total of 54
molecule equivalents required for the synthesis of one molecule of glucose.
This process is a fundamental and efficient way for cells to generate the
molecular energy that they require.
Plants, like this oak tree and acorn, use energy from
sunlight to make sugar and other organic molecules.
Both plants and animals (like this squirrel) use cellular
respiration to derive energy from the organic molecules
originally produced by plants. (credit “acorn”:
modification of work by Noel Reynolds; credit
“squirrel”: modification of work by Dawn Huczek)
Metabolic Pathways
The processes of making and breaking down sugar molecules illustrate two
types of metabolic pathways. A metabolic pathway is a series of
interconnected biochemical reactions that convert a substrate molecule or
molecules, step-by-step, through a series of metabolic intermediates,
eventually yielding a final product or products. In the case of sugar
metabolism, the first metabolic pathway synthesized sugar from smaller
molecules, and the other pathway broke sugar down into smaller molecules.
These two opposite processes—the first requiring energy and the second
producing energy—are referred to as anabolic (building) and catabolic
(breaking down) pathways, respectively. Consequently, metabolism is
composed of building (anabolism) and degradation (catabolism).
Note:
Evolution Connection
This tree shows the evolution of the various branches of
life. The vertical dimension is time. Early life forms, in
blue, used anaerobic metabolism to obtain energy from
their surroundings.
Evolution of Metabolic Pathways
There is more to the complexity of metabolism than understanding the
metabolic pathways alone. Metabolic complexity varies from organism to
organism. Photosynthesis is the primary pathway in which photosynthetic
organisms like plants (the majority of global synthesis is done by
planktonic algae) harvest the sun’s energy and convert it into
carbohydrates. The by-product of photosynthesis is oxygen, required by
some cells to carry out cellular respiration. During cellular respiration,
oxygen aids in the catabolic breakdown of carbon compounds, like
carbohydrates. Among the products of this catabolism are CO, and ATP. In
addition, some eukaryotes perform catabolic processes without oxygen
(fermentation); that is, they perform or use anaerobic metabolism.
Organisms probably evolved anaerobic metabolism to survive (living
organisms came into existence about 3.8 billion years ago, when the
atmosphere lacked oxygen). Despite the differences between organisms
and the complexity of metabolism, researchers have found that all branches
of life share some of the same metabolic pathways, suggesting that all
organisms evolved from the same ancient common ancestor ({link]).
Evidence indicates that over time, the pathways diverged, adding
specialized enzymes to allow organisms to better adapt to their
environment, thus increasing their chance to survive. However, the
underlying principle remains that all organisms must harvest energy from
their environment and convert it to ATP to carry out cellular functions.
Anabolic and Catabolic Pathways
Anabolic pathways require an input of energy to synthesize complex
molecules from simpler ones. Synthesizing sugar from CO, is one example.
Other examples are the synthesis of large proteins from amino acid building
blocks, and the synthesis of new DNA strands from nucleic acid building
blocks. These biosynthetic processes are critical to the life of the cell, take
place constantly, and demand energy provided by ATP and other high-
energy molecules like NADH (nicotinamide adenine dinucleotide) and
NADPH ([link]).
ATP is an important molecule for cells to have in sufficient supply at all
times. The breakdown of sugars illustrates how a single molecule of
glucose can store enough energy to make a great deal of ATP, 36 to 38
molecules. This is a catabolic pathway. Catabolic pathways involve the
degradation (or breakdown) of complex molecules into simpler ones.
Molecular energy stored in the bonds of complex molecules is released in
catabolic pathways and harvested in such a way that it can be used to
produce ATP. Other energy-storing molecules, such as fats, are also broken
down through similar catabolic reactions to release energy and make ATP
(Link]).
It is important to know that the chemical reactions of metabolic pathways
don’t take place spontaneously. Each reaction step is facilitated, or
catalyzed, by a protein called an enzyme. Enzymes are important for
catalyzing all types of biological reactions—those that require energy as
well as those that release energy.
Metabolic pathways
Anabolic: Small molecules are assembled into large ones. Energy is required.
C) C) @ OC) +Energyle ees
Catabolic: Large molecules are broken down into small ones. Energy is released.
©0800 — © © © O +=»
Anabolic pathways are those that require energy to
synthesize larger molecules. Catabolic pathways
are those that generate energy by breaking down
larger molecules. Both types of pathways are
required for maintaining the cell’s energy balance.
Thermodynamics
Introduction
" A theory is the more impressive the greater the simplicity of its premises
is, the more different kinds of things it relates, and the more extended is its
area of applicability. Therefore the deep impression which classical
thermodynamics made upon me. It is the only physical theory of universal
content concerning which I am convinced that within the framework of the
applicability of its basic concepts, it will never be overthrown. " Albert
Einstein (1946)
That high praise from Einstein still rings true today; the laws of
thermodynamics can still explain many interactions, both in the biotic and
abiotic realms. Thermodynamics refers to the study of energy and energy
transfer involving physical matter. The matter and its environment relevant
to a particular case of energy transfer are classified as a system, and
everything outside of that system is called the surroundings. For instance,
when heating a pot of water on the stove, the system includes the stove, the
pot, and the water. Energy is transferred within the system (between the
stove, pot, and water). There are two types of systems: open and closed. An
open system is one in which energy can be transferred between the system
and its surroundings. The stovetop system is open because heat can be lost
into the air. A closed system is one that cannot transfer energy to its
surroundings.
Biological organisms are open systems. Energy is exchanged between them
and their surroundings, as they consume energy-storing molecules and
release energy to the environment by doing work. Like all things in the
physical world, energy is subject to the laws of physics. The laws of
thermodynamics govern the transfer of energy in and among all systems in
the universe.
The First Law of Thermodynamics
The first law of thermodynamics deals with the total amount of energy in
the universe. It states that this total amount of energy in the universe is
constant. In other words, there has always been, and always will be, exactly
the same amount of energy in the universe. Energy exists in many different
forms. According to the first law of thermodynamics, energy may be
transferred from place to place or transformed into different forms, but it
cannot be created or destroyed. The transfers and transformations of energy
take place around us all the time. Light bulbs transform electrical energy
into light energy. Gas stoves transform chemical energy from natural gas
into heat energy. Plants perform one of the most biologically useful energy
transformations on earth: that of converting the energy of sunlight into the
chemical energy stored within organic molecules. Some examples of energy
transformations are shown in [link].
The challenge for all living organisms is to obtain energy from their
surroundings in forms that they can transfer or transform into usable energy
to do work. Living cells have evolved to meet this challenge very well.
Chemical energy stored within organic molecules such as sugars and fats is
transformed through a series of cellular chemical reactions into energy
within molecules of ATP. Energy in ATP molecules is easily accessible to
do work. Examples of the types of work that cells need to do include
building complex molecules, transporting materials, powering the beating
motion of cilia or flagella, contracting muscle fibers to create movement,
and reproduction.
Chemical energy Light energy
>» >
Kinetic energy Chemical energy
Shown are two examples of
energy being transferred from
one system to another and
transformed from one form to
another. Humans can convert
the chemical energy in food,
like this ice cream cone, into
kinetic energy (the energy of
movement to ride a bicycle).
Plants can convert
electromagnetic radiation (light
energy) from the sun into
chemical energy. (credit “ice
cream”: modification of work
by D. Sharon Pruitt; credit “kids
on bikes”: modification of work
by Michelle Riggen-Ransom;
credit “leaf”: modification of
work by Cory Zanker)
The Second Law of Thermodynamics
A living cell’s primary tasks of obtaining, transforming, and using energy to
do work may seem simple. However, the second law of thermodynamics
explains why these tasks are harder than they appear. None of the energy
transfers we’ve discussed, along with all energy transfers and
transformations in the universe, is completely efficient. In every energy
transfer, some amount of energy is lost in a form that is unusable. In most
cases, this form is heat energy. Thermodynamically, heat energy is defined
as the energy transferred from one system to another that is not doing work.
For example, when an airplane flies through the air, some of the energy of
the flying plane is lost as heat energy due to friction with the surrounding
air. This friction actually heats the air by temporarily increasing the speed
of air molecules. Likewise, some energy is lost as heat energy during
cellular metabolic reactions. This is good for warm-blooded creatures like
us, because heat energy helps to maintain our body temperature. Strictly
speaking, no energy transfer is completely efficient, because some energy is
lost in an unusable form.
An important concept in physical systems is that of order and disorder (also
known as randomness). The more energy that is lost by a system to its
surroundings, the less ordered and more random the system is. Scientists
refer to the measure of randomness or disorder within a system as entropy.
High entropy means high disorder and low energy ([link]). To better
understand entropy, think of a student’s bedroom. If no energy or work were
put into it, the room would quickly become messy. It would exist in a very
disordered state, one of high entropy. Energy must be put into the system, in
the form of the student doing work and putting everything away, in order to
bring the room back to a state of cleanliness and order. This state is one of
low entropy. Similarly, a car or house must be constantly maintained with
work in order to keep it in an ordered state. Left alone, the entropy of the
house or car gradually increases through rust and degradation. Molecules
and chemical reactions have varying amounts of entropy as well. For
example, as chemical reactions reach a state of equilibrium, entropy
increases, and as molecules at a high concentration in one place diffuse and
spread out, entropy also increases.
Note:
Scientific Connection
Transfer of Energy and the Resulting Entropy
Set up a simple experiment to understand how energy is transferred and
how a change in entropy results.
1. Take a block of ice. This is water in solid form, so it has a high
structural order. This means that the molecules cannot move very
much and are in a fixed position. The temperature of the ice is 0°C.
As aresult, the entropy of the system is low.
2. Allow the ice to melt at room temperature. What is the state of
molecules in the liquid water now? How did the energy transfer take
place? Is the entropy of the system higher or lower? Why?
3. Heat the water to its boiling point. What happens to the entropy of the
system when the water is heated?
All physical systems can be thought of in this way: Living things are highly
ordered, requiring constant energy input to be maintained in a state of low
entropy. As living systems take in energy-storing molecules and transform
them through chemical reactions, they lose some amount of usable energy
in the process, because no reaction is completely efficient. They also
produce waste and by-products that aren’t useful energy sources. This
process increases the entropy of the system’s surroundings. Since all energy
transfers result in the loss of some usable energy, the second law of
thermodynamics states that every energy transfer or transformation
increases the entropy of the universe. Even though living things are highly
ordered and maintain a state of low entropy, the entropy of the universe in
total is constantly increasing due to the loss of usable energy with each
energy transfer that occurs. Essentially, living things are in a continuous
uphill battle against this constant increase in universal entropy.
Increasing
entropy
Entropy is a measure of
randomness or disorder in a
system. Gases have higher
entropy than liquids, and liquids
have higher entropy than solids.
Potential, Kinetic, and Free Energy
Introduction
"Energie is the operation, efflux or activity of any being: as the light of the
Sunne is the energie of the Sunne, and every phantasm of the soul is the
energie of the soul. " Henry More (1642), this is the first recorded definition
of the term energy in English.
Energy is defined as the ability to do work. As you know, energy exists in
different forms. For example, chemical energy, electrical energy, light
energy, and heat energy are all different types of energy. While these are all
familiar types of energy that one can see or feel, there is another type of
energy that is much less tangible. This energy is associated with something
as simple as an object held above the ground. In order to appreciate the way
energy flows into and out of biological systems, it is important to
understand more about the different types of energy that exist in the
physical world.
Types of Energy
When an object is in motion, there is energy associated with that object. In
the example of an airplane in flight, there is a great deal of energy
associated with the motion of the airplane. This is because moving objects
are capable of enacting a change, or doing work. Think of a wrecking ball.
Even a slow-moving wrecking ball can do a great deal of damage to other
objects. However, a wrecking ball that is not in motion is incapable of
performing work. Energy associated with objects in motion is called kinetic
energy. A speeding bullet, a walking person, the rapid movement of
molecules in the air (which produces heat), and electromagnetic radiation
like light all have kinetic energy.
Now what if that same motionless wrecking ball is lifted two stories above
a car with a crane? If the suspended wrecking ball is unmoving, is there
energy associated with it? The answer is yes. The suspended wrecking ball
has energy associated with it that is fundamentally different from the kinetic
energy of objects in motion. This form of energy results from the fact that
there is the potential for the wrecking ball to do work. If it is released,
indeed it would do work. Because this type of energy refers to the potential
to do work, it is called potential energy. Objects transfer their energy
between kinetic and potential in the following way: As the wrecking ball
hangs motionless, it has 0 kinetic and 100 percent potential energy. Once it
is released, its kinetic energy begins to increase because it builds speed due
to gravity. At the same time, as it nears the ground, it loses potential energy.
Somewhere mid-fall it has 50 percent kinetic and 50 percent potential
energy. Just before it hits the ground, the ball has nearly lost its potential
energy and has near-maximal kinetic energy. Other examples of potential
energy include the energy of water held behind a dam ([link]), or a person
about to skydive out of an airplane.
Water behind a dam has potential energy. Moving water,
such as in a waterfall or a rapidly flowing river, has
kinetic energy. (credit “dam”: modification of work by
"Pascal"/Flickr; credit “waterfall”: modification of work
by Frank Gualtieri)
Potential energy is not only associated with the location of matter (such as a
child sitting on a tree branch), but also with the structure of matter. A spring
on the ground has potential energy if it is compressed; so does a rubber
band that is pulled taut. The very existence of living cells relies heavily on
structural potential energy. On a chemical level, the bonds that hold the
atoms of molecules together have potential energy. Remember that anabolic
cellular pathways require energy to synthesize complex molecules from
simpler ones, and catabolic pathways release energy when complex
molecules are broken down. The fact that energy can be released by the
breakdown of certain chemical bonds implies that those bonds have
potential energy. In fact, there is potential energy stored within the bonds of
all the food molecules we eat, which is eventually harnessed for use. This is
because these bonds can release energy when broken. The type of potential
energy that exists within chemical bonds, and is released when those bonds
are broken, is called chemical energy ([link]). Chemical energy is
responsible for providing living cells with energy from food. The release of
energy is brought about by breaking the molecular bonds within fuel
molecules.
The molecules in gasoline (octane,
the chemical formula shown)
contain chemical energy within
the chemical bonds. This energy is
transformed into kinetic energy
that allows a car to race on a
racetrack. (credit “car”:
modification of work by Russell
Trow)
Free Energy
After learning that chemical reactions release energy when energy-storing
bonds are broken, an important next question is how is the energy
associated with chemical reactions quantified and expressed? How can the
energy released from one reaction be compared to that of another reaction?
A measurement of free energy is used to quantitate these energy transfers.
Free energy is called Gibbs free energy (abbreviated with the letter G) after
Josiah Willard Gibbs, the scientist who developed the measurement. Recall
that according to the second law of thermodynamics, all energy transfers
involve the loss of some amount of energy in an unusable form such as
heat, resulting in entropy. Gibbs free energy specifically refers to the energy
associated with a chemical reaction that is available after entropy is
accounted for. In other words, Gibbs free energy is usable energy, or energy
that is available to do work. So, every chemical reaction involves a change
in free energy, called delta G (AG).
Endergonic Reactions and Exergonic Reactions
If energy is released during a chemical reaction, then the resulting value
from the above equation will be a negative number. In other words,
reactions that release energy have a AG < 0. A negative AG also means that
the products of the reaction have less free energy than the reactants, because
they gave off some free energy during the reaction. Reactions that have a
negative AG and consequently release free energy are called exergonic
reactions. Think: exergonic means energy is exiting the system. These
reactions are also referred to as spontaneous reactions, because they can
occur without the addition of energy into the system. Understanding which
chemical reactions are spontaneous and release free energy is extremely
useful for biologists, because these reactions can be harnessed to perform
work inside the cell. An important distinction must be drawn between the
term spontaneous and the idea of a chemical reaction that occurs
immediately. Contrary to the everyday use of the term, a spontaneous
reaction is not one that suddenly or quickly occurs. The rusting of iron is an
example of a spontaneous reaction that occurs slowly, little by little, over
time.
If a chemical reaction requires an input of energy rather than releasing
energy, then the AG for that reaction will be a positive value. In this case,
the products have more free energy than the reactants. Thus, the products of
these reactions can be thought of as energy-storing molecules. These
chemical reactions are called endergonic reactions, and they are non-
spontaneous. An endergonic reaction will not take place on its own without
the addition of free energy.
Let’s revisit the example of the synthesis and breakdown of the food
molecule, glucose. Remember that the building of complex molecules, such
as sugars, from simpler ones is an anabolic process and requires energy.
Therefore, the chemical reactions involved in anabolic processes are
endergonic reactions. On the other hand, the catabolic process of breaking
sugar down into simpler molecules releases energy in a series of exergonic
reactions. Like the example of rust above, the breakdown of sugar involves
spontaneous reactions, but these reactions don’t occur instantaneously.
[link] shows some other examples of endergonic and exergonic reactions.
Later sections will provide more information about what else is required to
make even spontaneous reactions happen more efficiently.
(c)
Shown are some examples of endergonic
processes (ones that require energy) and
exergonic processes (ones that release
energy). These include (a) a compost pile
decomposing, (b) a chick hatching from a
fertilized egg, (c) sand art being destroyed,
and (d) a ball rolling down a hill. (credit a:
modification of work by Natalie Maynor;
credit b: modification of work by USDA;
credit c: modification of work by
“Athlex”/Flickr; credit d: modification of
work by Harry Malsch)
An important concept in the study of metabolism and energy is that of
chemical equilibrium. Most chemical reactions are reversible. They can
proceed in both directions, releasing energy into their environment in one
direction, and absorbing it from the environment in the other direction
({link]). The same is true for the chemical reactions involved in cell
metabolism, such as the breaking down and building up of proteins into and
from individual amino acids, respectively. Reactants within a closed system
will undergo chemical reactions in both directions until a state of
equilibrium is reached. This state of equilibrium is one of the lowest
possible free energy and a state of maximal entropy. Energy must be put
into the system to push the reactants and products away from a state of
equilibrium. Either reactants or products must be added, removed, or
changed. If a cell were a closed system, its chemical reactions would reach
equilibrium, and it would die because there would be insufficient free
energy left to perform the work needed to maintain life. In a living cell,
chemical reactions are constantly moving towards equilibrium, but never
reach it. This is because a living cell is an open system. Materials pass in
and out, the cell recycles the products of certain chemical reactions into
other reactions, and chemical equilibrium is never reached. In this way,
living organisms are in a constant energy-requiring, uphill battle against
equilibrium and entropy. This constant supply of energy ultimately comes
from sunlight, which is used to produce nutrients in the process of
photosynthesis.
Energy is released Energy is added
reactants products
Gibbs Free Energy
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Exergonic and endergonic reactions result in changes in Gibbs
free energy. Exergonic reactions release energy; endergonic
reactions require energy to proceed.
Energy in Living Systems
Introduction
"There is deposited in them (plants) an enormous quantity of potential energy, whose equivalent is
provided to us as heat in the burning of a plant substance. So far as we know at present, the only
living energy absorbed during plant growth are the rays of sunlight... Animals take up oxygen and
complex oxidizable compounds made by plants, release largely as combustion products carbonic
acid and water, ...thus using a certain amount of chemical potential energy to produce heat and
mechanical forces." Hermann Ludwig Ferdinand von Helmholtz, 1847.
Energy production within a cell involves many coordinated chemical pathways. Most of these
pathways are combinations of oxidation and reduction reactions. Oxidation and reduction occur in
tandem. An oxidation reaction strips an electron from an atom in a compound, and the addition of
this electron to another compound is a reduction reaction. Because oxidation and reduction usually
occur together, these pairs of reactions are called oxidation reduction reactions, or redox reactions.
Electrons and Energy
The removal of an electron from a molecule, oxidizing it, results in a decrease in potential energy
in the oxidized compound. The electron (sometimes as part of a hydrogen atom), does not remain
unbonded, however, in the cytoplasm of a cell. Rather, the electron is shifted to a second
compound, reducing the second compound. The shift of an electron from one compound to another
removes some potential energy from the first compound (the oxidized compound) and increases the
potential energy of the second compound (the reduced compound)({link]). The transfer of electrons
between molecules is important because most of the energy stored in atoms and used to fuel cell
functions is in the form of high-energy electrons. The transfer of energy in the form of electrons
allows the cell to transfer and use energy in an incremental fashion—in small packages rather than
in a single, destructive burst. This section focuses on the extraction of energy from food; you will
see that as you track the path of the transfers, you are tracking the path of electrons moving through
metabolic pathways.
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Endergonic
Reduction
This image illustrates the coupling of oxidation and
reduction reactions. Molecule B is being oxidized to a
lower energy state while molecule D is being reduced to
a higher energy state. (Image by Robert Bear)
Electron Carriers
In living systems, a small class of compounds functions as electron shuttles: They bind and carry
high-energy electrons between compounds in pathways. The principal electron carriers we will
consider are derived from the B vitamin group and are derivatives of nucleotides. These
compounds can be easily reduced (that is, they accept electrons) or oxidized (they lose electrons).
Nicotinamide adenine dinucleotide (NAD) ([link]) is derived from vitamin B3, niacin. NAD* is the
oxidized form of the molecule; NADH is the reduced form of the molecule after it has accepted two
electrons and a proton (which together are the equivalent of a hydrogen atom with an extra
electron).
NAD* can accept electrons from an organic molecule according to the general equation:
Equation:
RH *
Reduci + ane —> See + -
educin
. ae Reduced Oxidized
agent agent
When electrons are added to a compound, they are reduced. A compound that reduces another is
called a reducing agent. In the above equation, RH is a reducing agent, and NAD* is reduced to
NADH. When electrons are removed from compound, it oxidized. A compound that oxidizes
another is called an oxidizing agent. In the above equation, NAD* is an oxidizing agent, and RH is
oxidized to R.
Similarly, flavin adenine dinucleotide (FAD*) is derived from vitamin By, also called riboflavin. Its
reduced form is FADH>. A second variation of NAD, NADP, contains an extra phosphate group.
Both NAD* and FAD* are extensively used in energy extraction from sugars, and NADP plays an
important role in anabolic reactions and photosynthesis.
The oxidized form of the electron carrier (NAD*) is
shown on the left and the reduced form (NADH) is
shown on the right. The nitrogenous base in NADH has
one more hydrogen ion and two more electrons than in
NAD".
Electron Transport Chain
The energy associated with high energy electrons is harvested in an incremental fashion, and
electron transport chains allow for this type of energy harvesting. An Electron Transport Chain is
a series of membrane bound proteins that are specialized in shuttling electrons ({link]). An electron
donor drops off high energy electrons and as the electrons pass from one protein to the next in the
chain, a small amount of energy is released. The energy release by each step is then available to do
work. After the electrons pass through the transport chain, the electrons are removed from the chain
and attached to the final electron acceptor. As you will see later in this module, electron transport
chains play an important role in the processes of photosynthesis and cellular respiration.
anes edie
Electron Donor Electron Acceptor
This image illustrates the release of energy (noted as
yellow and red stars) that is available to do work as
electrons pass from one protein to another in the electron
transport chain. (Image by Robert Bear)
ATP in Living Systems
A living cell cannot store significant amounts of free energy. Excess free energy would result in an
increase of heat in the cell, which would result in excessive thermal motion that could damage and
then destroy the cell. Rather, a cell must be able to handle that energy in a way that enables the cell
to store energy safely and release it for use only as needed. Living cells accomplish this by using
the compound adenosine triphosphate (ATP). ATP is often called the “energy currency” of the cell,
and, like currency, this versatile compound can be used to fill any energy need of the cell. How? It
functions similarly to a rechargeable battery.
When ATP is broken down, usually by the removal of its terminal phosphate group, energy is
released. The energy is used to do work by the cell, usually by the released phosphate binding to
another molecule, activating it. For example, in the mechanical work of muscle contraction, ATP
supplies the energy to move the contractile muscle proteins. Recall the active transport work of the
sodium-potassium pump in the biological membranes. ATP alters the structure of the integral
protein that functions as the pump, changing its affinity for sodium and potassium. In this way, the
cell performs work, pumping ions against their electrochemical gradients.
ATP Structure and Function
At the heart of ATP is a molecule of adenosine monophosphate (AMP), which is composed of an
adenine molecule bonded to a ribose molecule and to a single phosphate group ([link]). Ribose is a
five-carbon sugar found in RNA, and AMP is one of the nucleotides in RNA. The addition of a
second phosphate group by a condensation reaction to this core molecule results in the formation of
adenosine diphosphate (ADP); the addition of a third phosphate group by a condensation reaction
forms adenosine triphosphate (ATP).
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ATP (adenosine triphosphate) has three
phosphate groups that can be removed by
hydrolysis to form ADP (adenosine
diphosphate) or AMP (adenosine
monophosphate).The negative charges on
the phosphate group naturally repel each
other, requiring energy to bond them
together and releasing energy when these
bonds are broken.
The addition of a phosphate group to a molecule requires energy. Phosphate groups are negatively
charged and thus repel one another when they are arranged in series, as they are in ADP and ATP.
This repulsion makes the ADP and ATP molecules inherently unstable. The release of one or two
phosphate groups from ATP, a process called hydrolysis, releases energy.
ATP Powers Cellular Work
Hydrolysis is the process of breaking complex macromolecules apart. During hydrolysis, water is
split, or lysed, and the resulting hydrogen atom (H*) and a hydroxy] group (OH) are added to the
larger molecule. The hydrolysis of ATP produces ADP, together with an inorganic phosphate ion
(P;), and the release of free energy an exergonic reaction. This free energy is then available to drive
an endergonic reaction. The release of energy and absorption of this free energy is a coupled
reaction. To carry out life processes, ATP is continuously broken down into ADP, and like a
rechargeable battery, ADP is continuously regenerated into ATP by the reattachment of a third
phosphate group by a condensation reaction ([link]). Water, which was broken down into its
hydrogen atom and hydroxyl group during ATP hydrolysis, is reformed when a third phosphate is
added to the ADP molecule, reforming ATP with energy being absorbed. The energy necessary for
driving the formation of ATP comes from an exergonic reaction. Once again the coupling of an
exergonic reaction drives an endergonic reaction or the formation of ATP.
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This image illustrates the ATP cycle and how ATP couples the release of energy from one
reaction and makes that energy available for cellular work or endergonic reactions. (Image by
Robert Bear)
Obviously, energy must be infused into the system to regenerate ATP. Where does this energy come
from? In nearly every living thing on earth, the energy comes from the metabolism of glucose. In
this way, ATP is a direct link between the limited set of exergonic pathways of glucose catabolism
and the multitude of endergonic pathways that power living cells.
Phosphorylation
Recall that, in some chemical reactions, enzymes may bind to several substrates that react with
each other on the enzyme, forming an intermediate complex. An intermediate complex is a
temporary structure, and it allows one of the substrates (such as ATP) and reactants to more readily
react with each other; in reactions involving ATP, ATP is one of the substrates and ADP is a
product. During an endergonic chemical reaction, ATP forms an intermediate complex with the
substrate and enzyme in the reaction. This intermediate complex allows the ATP to transfer its third
phosphate group, with its energy, to the substrate, a process called phosphorylation.
Phosphorylation refers to the addition of the phosphate (~P). This is illustrated by the following
generic reaction:
Equation:
A+ enzyme + ATP > [A — enzyme — ~P] — B+ enzyme + ADP + phosphate ion
When the intermediate complex breaks apart, the energy is used to modify the substrate and convert
it into a product of the reaction. The ADP molecule and a free phosphate ion are released into the
medium and are available for recycling through cell metabolism.
Substrate Phosphorylation
ATP is generated through two mechanisms during the breakdown of glucose. A few ATP molecules
are generated (that is, regenerated from ADP) as a direct result of the chemical reactions that occur
in the catabolic pathways. A phosphate group is removed from an intermediate reactant in the
pathway, and the free energy of the reaction is used to add the third phosphate to an available ADP
molecule, producing ATP ({link]). This very direct method of phosphorylation is called substrate-
level phosphorylation.
In phosphorylation reactions, the gamma
phosphate of ATP is attached to a protein.
Oxidative Phosphorylation
Most of the ATP generated during glucose catabolism, however, is derived from a much more
complex process, chemiosmosis, which takes place in mitochondria ([link]) within a eukaryotic cell
or the plasma membrane of a prokaryotic cell. Chemiosmosis, a process of ATP production in
cellular metabolism, is used to generate 90 percent of the ATP made during glucose catabolism and
is also the method used in the light reactions of photosynthesis to harness the energy of sunlight.
The production of ATP using the process of chemiosmosis is called oxidative phosphorylation
because of the involvement of oxygen in the process.
ATP synthase enzymes and the
electron transport chain are
embedded in the inner membrane.
Intermembrane space
Matrix
Inner membrane
Outer membrane
In eukaryotes, oxidative
phosphorylation takes place in
mitochondria. In prokaryotes,
this process takes place in the
plasma membrane. (Credit:
modification of work by
Mariana Ruiz Villareal)
Cell Membranes and Passive Transport
Introduction
" A vital phenomenon can only be regarded as explained if it has been
proven that it appears as the result of the material components of living
organisms interacting according to the laws which those same components
follow in their interactions outside of living systems. " A. E. Fick, German
physiologist who developed the first mathematical explanation of diffusion
The simple diffusion model developed by Fick does indeed explain the
movement of molecules in both living and non-living systems. Molecules
move freely from an area of higher concentration to and area of lower
concentration, according to Fick's Law. Living organisms, however, impose
a barrier to diffusion of molecules into and from their cells - the plasma
membrane which surrounds all cells. Plasma membranes must allow certain
substances to enter and leave a cell, and prevent some harmful materials
from entering and some essential materials from leaving. In other words,
plasma membranes are selectively permeable—they allow some
substances to pass through, but not others. If they were to lose this
selectivity, the cell would no longer be able to sustain itself, and it would be
destroyed. Some cells require larger amounts of specific substances than do
other cells; they must have a way of obtaining these materials from
extracellular fluids. This may happen passively, as certain materials move
back and forth, or the cell may have special mechanisms that facilitate
transport. Some materials are so important to a cell that it spends some of
its energy, hydrolyzing adenosine triphosphate (ATP), to obtain these
materials. Red blood cells use some of their energy doing just that. All cells
spend the majority of their energy to maintain an imbalance of sodium and
potassium ions between the interior and exterior of the cell.
The most direct forms of membrane transport are passive. Passive
transport is a naturally occurring phenomenon and does not require the cell
to exert any of its energy to accomplish the movement. In passive transport,
substances move from an area of higher concentration to an area of lower
concentration. A physical space in which there is a range of concentrations
of a single substance is said to have a concentration gradient.
Selective Permeability
Plasma membranes are asymmetric: the interior of the membrane is not
identical to the exterior of the membrane. In fact, there is a considerable
difference between the array of phospholipids and proteins between the two
leaflets that form a membrane. On the interior of the membrane, some
proteins serve to anchor the membrane to fibers of the cytoskeleton. There
are peripheral proteins on the exterior of the membrane that bind elements
of the extracellular matrix. Carbohydrates, attached to lipids or proteins, are
also found on the exterior surface of the plasma membrane. These
carbohydrate complexes help the cell bind substances that the cell needs in
the extracellular fluid. This adds considerably to the selective nature of
plasma membranes ((Link]).
Glycoprotein: protein with Glycolipid: lipid with
| carbohydrate attached rh carbohydrate
attached
Peripheral membrane Phospholipid
protein bilayer
Integral membrane ali Protein channel
protein
Cytoskeletal filaments
The exterior surface of the plasma membrane is not identical to the
interior surface of the same membrane.
Recall that plasma membranes are amphiphilic: They have hydrophilic and
hydrophobic regions. This characteristic helps the movement of some
materials through the membrane and hinders the movement of others.
Lipid-soluble material with a low molecular weight can easily slip through
the hydrophobic lipid core of the membrane. Substances such as the fat-
soluble vitamins A, D, E, and K readily pass through the plasma
membranes in the digestive tract and other tissues. Fat-soluble drugs and
hormones also gain easy entry into cells and are readily transported into the
body’s tissues and organs. Molecules of oxygen and carbon dioxide have no
charge and so pass through membranes by simple diffusion.
Polar substances present problems for the membrane. While some polar
molecules connect easily with the outside of a cell, they cannot readily pass
through the lipid core of the plasma membrane. Additionally, while small
ions could easily slip through the spaces in the mosaic of the membrane,
their charge prevents them from doing so. Ions such as sodium, potassium,
calcium, and chloride must have special means of penetrating plasma
membranes. Simple sugars and amino acids also need help with transport
across plasma membranes, achieved by various transmembrane proteins
(channels).
Diffusion
Diffusion is a passive process of transport. A single substance tends to
move from an area of high concentration to an area of low concentration
until the concentration is equal across a space. You are familiar with
diffusion of substances through the air. For example, think about someone
opening a bottle of ammonia in a room filled with people. The ammonia gas
is at its highest concentration in the bottle; its lowest concentration is at the
edges of the room. The ammonia vapor will diffuse, or spread away, from
the bottle, and gradually, more and more people will smell the ammonia as
it spreads. Materials move within the cell’s cytosol by diffusion, and certain
materials move through the plasma membrane by diffusion ([link]).
Diffusion expends no energy. On the contrary, concentration gradients are a
form of potential energy, dissipated as the gradient is eliminated.
Lipid bilayer
(plasma
membrane)
Time
Diffusion through a permeable membrane moves a substance from an
area of high concentration (extracellular fluid, in this case) down its
concentration gradient (into the cytoplasm). (credit: modification of
work by Mariana Ruiz Villareal)
Each separate substance in a medium, such as the extracellular fluid, has its
own concentration gradient, independent of the concentration gradients of
other materials. In addition, each substance will diffuse according to that
gradient. Within a system, there will be different rates of diffusion of the
different substances in the medium.
Factors That Affect Diffusion
Molecules move constantly in a random manner, at a rate that depends on
their mass, their environment, and the amount of thermal energy they
possess, which in turn is a function of temperature. This movement
accounts for the diffusion of molecules through whatever medium in which
they are localized. A substance will tend to move into any space available
to it until it is evenly distributed throughout it. After a substance has
diffused completely through a space, removing its concentration gradient,
molecules will still move around in the space, but there will be no net
movement of the number of molecules from one area to another. This lack
of a concentration gradient in which there is no net movement of a
substance is known as dynamic equilibrium. While diffusion will go
forward in the presence of a concentration gradient of a substance, several
factors affect the rate of diffusion.
e Extent of the concentration gradient: The greater the difference in
concentration, the more rapid the diffusion. The closer the distribution
of the material gets to equilibrium, the slower the rate of diffusion
becomes.
e Mass of the molecules diffusing: Heavier molecules move more
slowly; therefore, they diffuse more slowly. The reverse is true for
lighter molecules.
e Temperature: Higher temperatures increase the energy and therefore
the movement of the molecules, increasing the rate of diffusion. Lower
temperatures decrease the energy of the molecules, thus decreasing the
rate of diffusion.
e Solvent density: As the density of a solvent increases, the rate of
diffusion decreases. The molecules slow down because they have a
more difficult time getting through the denser medium. If the medium
is less dense, diffusion increases. Because cells primarily use diffusion
to move materials within the cytoplasm, any increase in the
cytoplasm’s density will inhibit the movement of the materials. An
example of this is a person experiencing dehydration. As the body’s
cells lose water, the rate of diffusion decreases in the cytoplasm, and
the cells’ functions deteriorate. Neurons tend to be very sensitive to
this effect. Dehydration frequently leads to unconsciousness and
possibly coma because of the decrease in diffusion rate within the
cells.
e Solubility: As discussed earlier, nonpolar or lipid-soluble materials
pass through plasma membranes more easily than polar materials,
allowing a faster rate of diffusion.
e Surface area and thickness of the plasma membrane: Increased surface
area increases the rate of diffusion, whereas a thicker membrane
reduces it.
e Distance travelled: The greater the distance that a substance must
travel, the slower the rate of diffusion. This places an upper limitation
on cell size. A large, spherical cell will die because nutrients or waste
cannot reach or leave the center of the cell, respectively. Therefore,
cells must either be small in size, as in the case of many prokaryotes,
or be flattened, as with many single-celled eukaryotes.
A variation of diffusion is the process of filtration. In filtration, material
moves according to its concentration gradient through a membrane;
sometimes the rate of diffusion is enhanced by pressure, causing the
substances to filter more rapidly. This occurs in the kidney, where blood
pressure forces large amounts of water and accompanying dissolved
substances, or solutes, out of the blood and into the renal tubules. The rate
of diffusion in this instance is almost totally dependent on pressure. One of
the effects of high blood pressure is the appearance of protein in the urine,
which is “squeezed through” by the abnormally high pressure.
Facilitated diffusion
In facilitated diffusion, also called facilitated transport, materials diffuse
across the plasma membrane with the help of membrane proteins. A
concentration gradient exists that would allow these materials to diffuse into
the cell without expending cellular energy. However, these materials are
ions or polar molecules that are repelled by the hydrophobic parts of the
biological membrane. Facilitated diffusion proteins shield these materials
from the repulsive force of the membrane, allowing them to diffuse into the
cell.
The material being transported is first attached to protein or glycoprotein
receptors on the exterior surface of the plasma membrane. This allows the
material that is needed by the cell to be removed from the extracellular
fluid. The substances are then passed to specific integral proteins that
facilitate their passage. Some of these integral proteins are collections of
beta pleated sheets that form a pore or channel through the phospholipid
bilayer. Others are carrier proteins which bind with the substance and aid its
diffusion through the membrane.
Channels
The integral proteins involved in facilitated diffusion are collectively
referred to as transport proteins, and they function as either channels for
the material or carriers. In both cases, they are transmembrane proteins.
Channels are specific for the substance that is being transported. Channel
proteins have hydrophilic domains exposed to the intracellular and
extracellular fluids; they additionally have a hydrophilic channel through
their core that provides a hydrated opening through the membrane layers
({link]). Passage through the channel allows polar compounds to avoid the
nonpolar central layer of the plasma membrane that would otherwise slow
or prevent their entry into the cell. Aquaporins are channel proteins that
allow water to pass through the membrane at a very high rate.
Extracellular fluid
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Protein
channel
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a
Cytoplasm
Facilitated diffusion moves
substances down their
concentration gradients. They may
cross the plasma membrane with
the aid of channel proteins. (credit:
modification of work by Mariana
Ruiz Villareal)
Channel proteins are either open at all times or they are “gated,” which
controls the opening of the channel. The attachment of a particular ion to
the channel protein may control the opening, or other mechanisms or
substances may be involved. In some tissues, sodium and chloride ions pass
freely through open channels, whereas in other tissues a gate must be
opened to allow passage. An example of this occurs in the kidney, where
both forms of channels are found in different parts of the renal tubules.
Cells involved in the transmission of electrical impulses, such as nerve and
muscle cells, have gated channels for sodium, potassium, and calcium in
their membranes. Opening and closing of these channels changes the
relative concentrations on opposing sides of the membrane of these ions,
resulting in the facilitation of electrical transmission along membranes (in
the case of nerve cells) or in muscle contraction (in the case of muscle
cells).
Carrier Proteins
Another type of protein embedded in the plasma membrane is a carrier
protein. This aptly named protein binds a substance and, in doing so,
triggers a change of its own shape, moving the bound molecule from the
outside of the cell to its interior ({link]); depending on the gradient, the
material may move in the opposite direction. Carrier proteins are typically
specific for a single substance. This selectivity adds to the overall
selectivity of the plasma membrane. The exact mechanism for the change of
shape is poorly understood. Proteins can change shape when their hydrogen
bonds are affected, but this may not fully explain this mechanism. Each
carrier protein is specific to one substance, and there are a finite number of
these proteins in any membrane. This can cause problems in transporting
enough of the material for the cell to function properly. When all of the
proteins are bound to their ligands, they are saturated and the rate of
transport is at its maximum. Increasing the concentration gradient at this
point will not result in an increased rate of transport.
Extracellular fluid
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Some substances are able to move down their concentration gradient
across the plasma membrane with the aid of carrier proteins. Carrier
proteins change shape as they move molecules across the membrane.
(credit: modification of work by Mariana Ruiz Villareal)
An example of this process occurs in the kidney. Glucose, water, salts, ions,
and amino acids needed by the body are filtered in one part of the kidney.
This filtrate, which includes glucose, is then reabsorbed in another part of
the kidney. Because there are only a finite number of carrier proteins for
glucose, if more glucose is present than the proteins can handle, the excess
is not transported and it is excreted from the body in the urine. In a diabetic
individual, this is described as “spilling glucose into the urine.” A different
group of carrier proteins called glucose transport proteins, or GLUTs, are
involved in transporting glucose and other hexose sugars through plasma
membranes within the body.
Channel and carrier proteins transport material at different rates. Channel
proteins transport much more quickly than do carrier proteins. Channel
proteins facilitate diffusion at a rate of tens of millions of molecules per
second, whereas carrier proteins work at a rate of a thousand to a million
molecules per second.
Osmosis
Osmosis is the movement of water through a semipermeable membrane
according to the concentration gradient of water across the membrane,
which is inversely proportional to the concentration of solutes. While
diffusion transports material across membranes and within cells, osmosis
transports only water across a membrane and the membrane limits the
diffusion of solutes in the water. Not surprisingly, the aquaporins that
facilitate water movement play a large role in osmosis, most prominently in
red blood cells and the membranes of kidney tubules.
Mechanism
Osmosis is a special case of diffusion. Water, like other substances, moves
from an area of high concentration to one of low concentration. An obvious
question is what makes water move at all? Imagine a beaker with a
semipermeable membrane separating the two sides or halves ([link]). On
both sides of the membrane the water level is the same, but there are
different concentrations of a dissolved substance, or solute, that cannot
cross the membrane (otherwise the concentrations on each side would be
balanced by the solute crossing the membrane). If the volume of the
solution on both sides of the membrane is the same, but the concentrations
of solute are different, then there are different amounts of water, the solvent,
on either side of the membrane.
Semipermeable membrane
In osmosis, water always moves
from an area of higher water
concentration to one of lower
concentration. In the diagram
shown, the solute cannot pass
through the selectively permeable
membrane, but the water can.
To illustrate this, imagine two full glasses of water. One has a single
teaspoon of sugar in it, whereas the second one contains one-quarter cup of
sugar. If the total volume of the solutions in both cups is the same, which
cup contains more water? Because the large amount of sugar in the second
cup takes up much more space than the teaspoon of sugar in the first cup,
the first cup has more water in it.
Returning to the beaker example, recall that it has a mixture of solutes on
either side of the membrane. A principle of diffusion is that the molecules
move around and will spread evenly throughout the medium if they can.
However, only the material capable of getting through the membrane will
diffuse through it. In this example, the solute cannot diffuse through the
membrane, but the water can. Water has a concentration gradient in this
system. Thus, water will diffuse down its concentration gradient, crossing
the membrane to the side where it is less concentrated. This diffusion of
water through the membrane—osmosis—will continue until the
concentration gradient of water goes to zero or until the hydrostatic pressure
of the water balances the osmotic pressure. Osmosis proceeds constantly in
living systems.
Tonicity
Tonicity is a measure of the osmotic pressure of two solutions separated by
a semipermeable membrane. So, tonicity describes how an extracellular
solution can change the volume of a cell by affecting osmosis. A solution's
tonicity often directly correlates with the osmolarity of the solution.
Osmolarity describes the total solute concentration of the solution. A
solution with low osmolarity has a greater number of water molecules
relative to the number of solute particles; a solution with high osmolarity
has fewer water molecules with respect to solute particles. In a situation in
which solutions of two different osmolarities are separated by a membrane
permeable to water, though not to the solute, water will move from the side
of the membrane with lower osmolarity (and more water) to the side with
higher osmolarity (and less water). This effect makes sense if you
remember that the solute cannot move across the membrane, and thus the
only component in the system that can move—the water—moves along its
own concentration gradient. An important distinction that concerns living
systems is that osmolarity measures the number of particles (which may be
molecules) in a solution. Therefore, a solution that is cloudy with cells may
have a lower osmolarity than a solution that is clear, if the second solution
contains more dissolved molecules than there are cells.
Hypotonic Solutions
Three terms—hypotonic, isotonic, and hypertonic—are used to relate the
osmolarity of a cell to the osmolarity of the extracellular fluid that contains
the cells. In a hypotonic situation, the extracellular fluid has lower
osmolarity than the fluid inside the cell, and water enters the cell. (In living
systems, the point of reference is always the cytoplasm, so the prefix hypo-
means that the extracellular fluid has a lower concentration of solutes, or a
lower osmolarity, than the cell cytoplasm.) It also means that the
extracellular fluid has a higher concentration of water in the solution than
does the cell. In this situation, water will follow its concentration gradient
and enter the cell.
Hypertonic Solutions
As for a hypertonic solution, the prefix hyper- refers to the extracellular
fluid having a higher osmolarity than the cell’s cytoplasm; therefore, the
fluid contains less water than the cell does. Because the cell has a relatively
higher concentration of water, water will leave the cell.
Isotonic Solutions
In an isotonic solution, the extracellular fluid has the same osmolarity as
the cell. If the osmolarity of the cell matches that of the extracellular fluid,
there will be no net movement of water into or out of the cell, although
water will still move in and out. Blood cells and plant cells in hypertonic,
isotonic, and hypotonic solutions take on characteristic appearances ({link]).
Hypertonic Isotonic Hypotonic
—e Ss *@®
Osmotic pressure changes the
shape of red blood cells in
hypertonic, isotonic, and
hypotonic solutions. (credit:
Mariana Ruiz Villareal)
Tonicity in Living Systems
In a hypotonic environment, water enters a cell, and the cell swells. In an
isotonic condition, the relative concentrations of solute and solvent are
equal on both sides of the membrane. There is no net water movement;
therefore, there is no change in the size of the cell. In a hypertonic solution,
water leaves a cell and the cell shrinks. If either the hypo- or hyper-
condition goes to excess, the cell’s functions become compromised, and the
cell may be destroyed.
A red blood cell will burst, or lyse, when it swells beyond the plasma
membrane’s capability to expand. Remember, the membrane resembles a
mosaic, with discrete spaces between the molecules composing it. If the cell
swells, and the spaces between the lipids and proteins become too large, the
cell will break apart.
In contrast, when excessive amounts of water leave a red blood cell, the cell
shrinks, or crenates. This has the effect of concentrating the solutes left in
the cell, making the cytosol denser and interfering with diffusion within the
cell. The cell’s ability to function will be compromised and may also result
in the death of the cell.
Various living things have ways of controlling the effects of osmosis—a
mechanism called osmoregulation. Some organisms, such as plants, fungi,
bacteria, and some protists, have cell walls that surround the plasma
membrane and prevent cell lysis in a hypotonic solution. The plasma
membrane can only expand to the limit of the cell wall, so the cell will not
lyse. In fact, the cytoplasm in plants is always slightly hypertonic to the
cellular environment, and water will always enter a cell if water is
available. This inflow of water produces turgor pressure, which stiffens the
cell walls of the plant ({link]). In nonwoody plants, turgor pressure supports
the plant. Conversly, if the plant is not watered, the extracellular fluid will
become hypertonic, causing water to leave the cell. In this condition, the
cell does not shrink because the cell wall is not flexible. However, the
plasma membrane detaches from the wall and constricts the cytoplasm. This
is called plasmolysis. Plants lose turgor pressure in this condition and wilt
({link]).
Hypertonic lsotonic Hypotonic
Vacuole
HO
The turgor pressure within a plant
cell depends on the tonicity of the
solution that it is bathed in.
(credit: modification of work by
Mariana Ruiz Villareal)
Without adequate water, the plant on the left has lost turgor pressure,
visible in its wilting; the turgor pressure is restored by watering it
(right). (credit: Victor M. Vicente Selvas)
Tonicity is a concern for all living things. For example, paramecia and
amoebas, which are protists that lack cell walls, have contractile vacuoles.
This vesicle collects excess water from the cell and pumps it out, keeping
the cell from lysing as it takes on water from its environment ((Link]).
Contractile
vacuoles
A paramecium’s contractile vacuole,
here visualized using bright field light
microscopy at 480x magnification,
continuously pumps water out of the
organism’s body to keep it from
bursting in a hypotonic medium.
(credit: modification of work by NIH;
scale-bar data from Matt Russell)
Many marine invertebrates have internal salt levels matched to their
environments, making them isotonic with the water in which they live. Fish,
however, must spend approximately five percent of their metabolic energy
maintaining osmotic homeostasis. Freshwater fish live in an environment
that is hypotonic to their cells. These fish actively take in salt through their
gills and excrete diluted urine to rid themselves of excess water. Saltwater
fish live in the reverse environment, which is hypertonic to their cells, and
they secrete salt through their gills and excrete highly concentrated urine.
In vertebrates, the kidneys regulate the amount of water in the body.
Osmoreceptors are specialized cells in the brain that monitor the
concentration of solutes in the blood. If the levels of solutes increase
beyond a certain range, a hormone is released that retards water loss
through the kidney and dilutes the blood to safer levels. Animals also have
high concentrations of albumin, which is produced by the liver, in their
blood. This protein is too large to pass easily through plasma membranes
and is a major factor in controlling the osmotic pressures applied to tissues.
Energy Requiring Transport
Introduction
"Against the wind," "We were runnin’ against the wind," "We were young
and strong and we were runnin" "against the wind" - Bob Seger, chorus of
Against the Wind.
Active Transport
As the song says, you have to be strong to be moving against the wind.
And, at the cellular level, you have to have significant energy to move
materials against a concentration gradient. The process which cells use to
do that is called active transport. Active transport mechanisms require the
use of the cell’s energy, usually in the form of adenosine triphosphate
(ATP). If a substance must move into the cell against its concentration
gradient, that is, if the concentration of the substance inside the cell must be
greater than its concentration in the extracellular fluid, the cell must use
energy to move the substance. Some active transport mechanisms move
small-molecular weight material, such as ions, through the membrane.
In addition to moving small ions and molecules through the membrane,
cells also need to remove and take in larger molecules and particles. Some
cells are even capable of engulfing entire unicellular microorganisms. You
might have correctly hypothesized that the uptake and release of large
particles by the cell requires energy. A large particle, however, cannot pass
through the membrane, even with energy supplied by the cell.
Electrochemical Gradient
We have discussed simple concentration gradients—differential
concentrations of a substance across a space or a membrane—but in living
systems, gradients are more complex. Because cells contain proteins, most
of which are negatively charged, and because ions move into and out of
cells, there is an electrical gradient, a difference of charge, across the
plasma membrane. The interior of living cells is electrically negative with
respect to the extracellular fluid in which they are bathed; at the same time,
cells have higher concentrations of potassium (K*) and lower
concentrations of sodium (Na‘) than does the extracellular fluid. Thus, in a
living cell, the concentration gradient and electrical gradient of Na*
promotes diffusion of the ion into the cell, and the electrical gradient of Na*
(a positive ion) tends to drive it inward to the negatively charged interior.
The situation is more complex, however, for other elements such as
potassium. The electrical gradient of K* promotes diffusion of the ion into
the cell, but the concentration gradient of K* promotes diffusion out of the
cell ({link]). The combined gradient that affects an ion is called its
electrochemical gradient, and it is especially important to muscle and
nerve cells.
kj Net Charge —
Electrochemical gradients arise from the
combined effects of concentration gradients and
electrical gradients. (credit: modification of
work by “Synaptitude”/Wikimedia Commons)
Moving Against a Gradient
To move substances against a concentration or an electrochemical gradient,
the cell must use energy. This energy is harvested from ATP that is
generated through cellular metabolism. Active transport mechanisms,
collectively called pumps or carrier proteins, work against electrochemical
gradients. With the exception of ions, small substances constantly pass
through plasma membranes. Active transport maintains concentrations of
ions and other substances needed by living cells in the face of these passive
changes. Much of a cell’s supply of metabolic energy may be spent
maintaining these processes. Because active transport mechanisms depend
on cellular metabolism for energy, they are sensitive to many metabolic
poisons that interfere with the supply of ATP.
Two mechanisms exist for the transport of small-molecular weight material
and macromolecules. Primary active transport moves ions across a
membrane and creates a difference in charge across that membrane. The
primary active transport system uses ATP to move a substance, such as an
ion, into the cell, and often at the same time, a second substance is moved
out of the cell. The sodium-potassium pump, an important pump in animal
cells, expends energy to move potassium ions into the cell and a different
number of sodium ions out of the cell ({link]). The action of this pump
results in a concentration and charge difference across the membrane.
Extracellular space
@ QO Na*
. @
ons Q @ oe: “ @
e. 78 @ @
coe] AGRON TOOT Ti
- oF HUE ULL UU
Phosphate ““@
od
. e
Cytoplasm K*
The sodium-potassium pump move potassium and sodium ions
across the plasma membrane. (credit: modification of work by
Mariana Ruiz Villarreal)
Secondary active transport describes the movement of material using the
energy of the electrochemical gradient established by primary active
transport. Using the energy of the electrochemical gradient created by the
primary active transport system, other substances such as amino acids and
glucose can be brought into the cell through membrane channels. ATP itself
is formed through secondary active transport using a hydrogen ion gradient
in the mitochondrion.
Bulk Transport of Materials
Endocytosis
Endocytosis is a type of energy requiring transport that moves particles,
such as large molecules, parts of cells, and even whole cells, into a cell.
There are different variations of endocytosis, but all share a common
characteristic: The plasma membrane of the cell invaginates, forming a
pocket around the target particle. The pocket pinches off, resulting in the
particle being contained in a newly created vacuole that is formed from the
plasma membrane.
Phagocytosis Pinocytosis Receptor-mediated
endocytosis
coed
s
" » *
rs Large particle *
P . x" *
A
Plasma
membrane
Clathrin Receptor
©
Vacuole
©...
Coated vesicle
(a) (b) (©)
Three variations of endocytosis are shown. (a) In one form of
endocytosis, phagocytosis, the plasma membrane surrounds the
particle and pinches off to form an intracellular vacuole. (b) In
another type of endocytosis, pinocytosis, the cell membrane
surrounds a small volume of fluid and pinches off, forming a
vesicle. (c) In receptor-mediated endocytosis, uptake of substances
by the cell is targeted to a single type of substance that binds at the
receptor on the plasma membrane. (credit: modification of work
by Mariana Ruiz Villarreal)
Phagocytosis is the process by which large particles, such as cells, are
taken in by a cell. For example, when microorganisms invade the human
body, a type of white blood cell called a neutrophil removes the invader
through this process, surrounding and engulfing the microorganism, which
is then destroyed by the neutrophil ((link]).
A variation of endocytosis is called pinocytosis. This literally means “cell
drinking” and was named at a time when the assumption was that the cell
was purposefully taking in extracellular fluid. In reality, this process takes
in solutes that the cell needs from the extracellular fluid ((link]).
A targeted variation of endocytosis employs binding proteins in the plasma
membrane that are specific for certain substances ({link]). The particles
bind to the proteins and the plasma membrane invaginates, bringing the
substance and the proteins into the cell. If passage across the membrane of
the target of receptor-mediated endocytosis is ineffective, it will not be
removed from the tissue fluids or blood. Instead, it will stay in those fluids
and increase in concentration. Some human diseases are caused by a failure
of receptor-mediated endocytosis. For example, the form of cholesterol
termed low-density lipoprotein or LDL (also referred to as “bad”
cholesterol) is removed from the blood by receptor-mediated endocytosis.
In the human genetic disease familial hypercholesterolemia, the LDL
receptors are defective or missing entirely. People with this condition have
life-threatening levels of cholesterol in their blood, because their cells
cannot clear the chemical from their blood.
Exocytosis
In contrast to these methods of moving material into a cell is the process of
exocytosis. Exocytosis is the opposite of the processes discussed above in
that its purpose is to expel material from the cell into the extracellular fluid.
A particle enveloped in membrane fuses with the interior of the plasma
membrane. This fusion opens the membranous envelope to the exterior of
the cell, and the particle is expelled into the extracellular space ([link]).
Exocytosis
Extracellular fluid
SS Cyctoplasm
Vesicle
In exocytosis, a vesicle
migrates to the plasma
membrane, binds, and
releases its contents to the
outside of the cell. (credit:
modification of work by
Mariana Ruiz Villarreal)
Overview of Photosynthesis
Introduction
"Nature has put itself the problem how to catch in flight light streaming to
the earth and to store the most elusive of all powers in rigid form. To
achieve this aim, it has covered the crust of earth with organisms which in
their life processes absorb the light of the sun and use this power to produce
a continuously accumulating chemical difference. ... The plants take in one
form of power, light; and produce another power, chemical difference. "
Robert Mayer, German physicist who developed the concept of the
conservation of heat, 1845
The sun not only provides the energy for the plants themselves, but for all
other creatures on the planet. Indeed, ancient photosynthesis provided the
fossil fuel energy that we use to generate electricity or power our cars. Each
cell in every organism runs on the chemical energy found mainly in
carbohydrate molecules (food), and the majority of these molecules are
produced by one process: photosynthesis. Through photosynthesis, certain
organisms convert solar energy (sunlight) into chemical energy, which is
then used to build carbohydrate molecules. The energy used to hold these
molecules together is released when an organism breaks down food during
cellular respiration. Cells then use this energy to perform work, such as
movement.
The energy that is harnessed from photosynthesis enters the ecosystems of
our planet continuously and is transferred from one organism to another
until almost all of the harvested energy is transferred and released as heat
energy. Therefore, directly or indirectly, the process of photosynthesis
provides most of the energy required by living things on earth ((link]).
Co,
Glucose ad
Sunlight--> t= ae ==> Heat
Autotrophs Heterotrophs
/
4
be HO
Heat
This image shows the role of photosynthesis is the flow of energy
through and ecosystem. Light energy enters the system through
photosynthesis and leaves primarily as heat energy once the energy is
used by organisms. (image by Eva Horne and Robert Bear)
Photosynthesis also results in the release of oxygen into the atmosphere. In
short, to eat and breathe, humans depend almost entirely on the organisms
that carry out photosynthesis.
Solar Dependence and Food Production
Some organisms can carry out photosynthesis, whereas others cannot. An
autotroph is an organism that can produce its own food. The Greek roots of
the word autotroph mean “self” (auto) “feeder” (troph). Plants are the best-
known autotrophs, but others exist, including certain types of bacteria and
algae ({link]). Oceanic algae contribute enormous quantities of food and
oxygen to global food chains. Plants are also photoautotrophs, a type of
autotroph that uses sunlight and carbon from carbon dioxide to synthesize
chemical energy in the form of carbohydrates. All organisms carrying out
photosynthesis require sunlight.
2 See
(a) (b) (c)
(a) Plants, (b) algae, and (c) certain bacteria, called cyanobacteria, are
photoautotrophs that can carry out photosynthesis. Algae can grow
Over enormous areas in water, at times completely covering the
surface. (credit a: Steve Hillebrand, U.S. Fish and Wildlife Service;
credit b: "eutrophication&hypoxia"/Flickr; credit c: NASA; scale-bar
data from Matt Russell)
Heterotrophs are organisms incapable of photosynthesis that must
therefore obtain energy and carbon from food by consuming other
organisms. The Greek roots of the word heterotroph mean “other” (hetero)
“feeder” (troph), meaning that their food comes from other organisms. Even
if the food organism is another animal, this food traces its origins back to
autotrophs and the process of photosynthesis. Humans are heterotrophs, as
are all animals. Heterotrophs depend on autotrophs, either directly or
indirectly. Deer and wolves are heterotrophs. A deer obtains energy by
eating plants. A wolf eating a deer obtains energy that originally came from
the plants eaten by that deer. The energy in the plant came from
photosynthesis, and therefore it is the only autotroph in this example. Using
this reasoning, all food eaten by humans also links back to autotrophs that
carry out photosynthesis.
The Flow of Energy
Whether the organism is a bacterium, plant, or animal, all living things
access energy by breaking down carbohydrate molecules. But if plants
make carbohydrate molecules, why would they need to break them down,
especially when it has been shown that the gas organisms release as a
“waste product” (CO>) acts as a substrate for the formation of more food in
photosynthesis? Remember, living things need energy to perform life
functions. In addition, an organism can either make its own food or eat
another organism—either way, the food still needs to be broken down.
Finally, in the process of breaking down food, called cellular respiration,
heterotrophs release needed energy and produce “waste” in the form of CO»
gas.
In nature, there is no such thing as waste. Every single atom of matter and
energy is conserved, recycling over and over infinitely. Substances change
form or move from one type of molecule to another, but their constituent
atoms never disappear.
CO, is no more a form of waste than oxygen is form of waste from
photosynthesis. Both are byproducts of reactions and move on to other
reactions. Photosynthesis absorbs light energy to build carbohydrates in
chloroplasts, and aerobic cellular respiration releases energy by using
oxygen to take metabolize carbohydrates in the cytoplasm and
mitochondria([link]). Both processes use electron transport chains to
capture the energy necessary to drive the reactions, because breaking down
a substance requires energy. These two powerhouse processes,
photosynthesis and cellular respiration, function in biological, cyclical
harmony to allow organisms to access life-sustaining energy that originates
millions of miles away in a burning star humans call the sun.
Photosynthesis which occurs in the chloroplast consumes
carbon dioxide and water while producing carbohydrates
(glucose) and oxygen while Aerobic Cellular respiration
which occurs in the mitochondria consumes glucose and
oxygen while producing carbohydrates. (Image by Eva
Horne and Robert Bear)
Main Structures and Summary of Photosynthesis
Photosynthesis requires sunlight, carbon dioxide, and water as starting
reactants ({link]). After the process is complete, photosynthesis releases
oxygen and produces carbohydrate molecules, most commonly glucose.
These sugar molecules contain the energy that living things need to survive.
Mcarbon dione]
a
ech
- PHOTOSYNTHESIS
Photosynthesis uses solar energy,
carbon dioxide, and water to release
oxygen and to produce energy-storing
sugar molecules.
The
complex reactions of photosynthesis can be summarized by the
chemical equation shown in [Link].
Energy
Carbon
Diode + Water + Sunlight Glucose + Oxygen
The process of photosynthesis can be
represented by an equation, wherein carbon
dioxide and water produce sugar and oxygen
using energy from sunlight. Since the
products have a higher energy level than the
reactants, photosynthesis is an endergonic
reaction. (Image by Robert Bear)
Although the equation looks simple, the many steps that take place during
photosynthesis are actually quite complex, as in the way that the reaction
summarizing cellular respiration represented many individual reactions.
Before learning the details of how photoautotrophs turn sunlight into food,
it is important to become familiar with the physical structures involved.
In plants, photosynthesis takes place primarily in leaves, which consist of
many layers of cells and have differentiated top and bottom sides. The
process of photosynthesis occurs not on the surface layers of the leaf, but
rather in a middle layer called the mesophyll ((link]). The gas exchange of
carbon dioxide and oxygen occurs through small, regulated openings called
stomata.
In all autotrophic eukaryotes, photosynthesis takes place inside an organelle
called a chloroplast. In plants, chloroplast-containing cells exist in the
mesophyll. Chloroplasts have a double (inner and outer) membrane. Within
the chloroplast is a third membrane that forms stacked, disc-shaped
structures called thylakoids. Embedded in the thylakoid membrane are
molecules of chlorophyll, a pigment (a molecule that absorbs light)
through which the entire process of photosynthesis begins. Chlorophyll is
responsible for the green color of plants. The thylakoid membrane encloses
an internal space called the thylakoid space. Other types of pigments exist
that can carry out photosynthesis, but chlorophyll is by far the most
common. As shown in [link], a stack of thylakoids is called granum, and
the space surrounding the granum is called stroma (not to be confused with
stomata, the openings on the leaves).
Upper
epidermis
Mesophyll
Stomata 7
Chloroplast
Outer
membrane
J
IN 7 hylakoids
Stroma
Not all cells of a leaf carry out
photosynthesis. Cells within the
middle layer of a leaf have
chloroplasts, which contain the
photosynthetic apparatus. (credit
"leaf": modification of work by Cory
Zanker)
The Two Parts of Photosynthesis
Photosynthesis takes place in two stages: the light-dependent reactions and
the Calvin cycle ({link]). In the light-dependent reactions, which take
place at the thylakoid membrane, chlorophyll absorbs energy from sunlight
and then converts it into chemical energy with the use of water. The light-
dependent reactions release oxygen from the hydrolysis of water as a
byproduct. In the Calvin cycle, which takes place in the stroma, the
chemical energy derived from the light-dependent reactions drives both the
capture of carbon in carbon dioxide molecules and the subsequent assembly
of sugar molecules. The two reactions use carrier molecules to transport the
energy from one to the other. The carriers that move energy from the light-
dependent reactions to the Calvin cycle reactions can be thought of as “full”
because they bring energy. After the energy is released, the “empty” energy
carriers return to the light-dependent reactions to obtain more energy.
The process of photosynthesis is divided to two stages that are linked
by the energy and electron carriers ATP and NADPH. (Image by Eva
Horne and Robert Bear)
The Light-Dependent Reactions
Introduction
"And God said, Let there be light: and there was light." The Book of
Genesis 1:3
It is interesting that light is one of the first things mentioned in the Bible,
since light indeed has to be present before any of the other creatures, plant
or animal, become possible. The light from the sun powers every cell on the
planet, allowing plants to make food that the rest of us can also partake of.
How can light be used to make food? When a person turns on a lamp,
electrical energy becomes light energy. Like all other forms of kinetic
energy, light can travel, change form, and be harnessed to do work. In the
case of photosynthesis, light energy is converted into chemical energy,
which photoautotrophs use to build carbohydrate molecules ({link]).
However, autotrophs only use a few specific components of sunlight.
Photoautotrophs can capture
light energy from the sun,
converting it into the chemical
energy used to build food
molecules. (credit: Gerry
Atwell)
What Is Light Energy?
The sun emits an enormous amount of electromagnetic radiation (solar
energy). Humans can see only a fraction of this energy, which portion is
therefore referred to as “visible light.” The manner in which solar energy
travels is described as waves. Scientists can determine the amount of energy
of a wave by measuring its wavelength, the distance between consecutive
points of a wave. A single wave is measured from two consecutive points,
such as from crest to crest or from trough to trough ([link]).
Energy Wave
Wavelength
The wavelength of a single wave
is the distance between two
consecutive points of similar
position (two crests or two
troughs) along the wave.
Visible light constitutes only one of many types of electromagnetic
radiation emitted from the sun and other stars. Scientists differentiate the
various types of radiant energy from the sun within the electromagnetic
spectrum. The electromagnetic spectrum is the range of all possible
frequencies of radiation ({link]). The difference between wavelengths
relates to the amount of energy carried by them.
Green Yellow Orange Red
GAMMA RAYS X-RAYS UV [VISIBLET INFRARED
WAVELENGTH
The sun emits energy in the form of electromagnetic radiation. This
radiation exists at different wavelengths, each of which has its own
characteristic energy. All electromagnetic radiation, including visible
light, is characterized by its wavelength.
Each type of electromagnetic radiation travels at a particular wavelength.
The longer the wavelength (or the more stretched out it appears in the
diagram), the less energy is carried. Short, tight waves carry the most
energy. This may seem illogical, but think of it in terms of a piece of
moving a heavy rope. It takes little effort by a person to move a rope in
long, wide waves. To make a rope move in short, tight waves, a person
would need to apply significantly more energy.
The electromagnetic spectrum ([link]) shows several types of
electromagnetic radiation originating from the sun, including X-rays and
ultraviolet (UV) rays. The higher-energy waves can penetrate tissues and
damage cells and DNA, explaining why both X-rays and UV rays can be
harmful to living organisms.
Absorption of Light
Light energy initiates the process of photosynthesis when pigments absorb
the light. Organic pigments, whether in the human retina or the chloroplast
thylakoid, have a narrow range of energy levels that they can absorb.
Energy levels lower than those represented by red light are insufficient to
raise an orbital electron to a populatable, excited (quantum) state. Energy
levels higher than those in blue light will physically tear the molecules
apart, called bleaching. So retinal pigments can only “see” (absorb) 700 nm
to 400 nm light, which is therefore called visible light. For the same
reasons, plants pigment molecules absorb only light in the wavelength
range of 700 nm to 400 nm; plant physiologists refer to this range for plants
as photosynthetically active radiation.
The visible light seen by humans as white light actually exists in a rainbow
of colors. Certain objects, such as a prism or a drop of water, disperse white
light to reveal the colors to the human eye. The visible light portion of the
electromagnetic spectrum shows the rainbow of colors, with violet and blue
having shorter wavelengths, and therefore higher energy. At the other end
of the spectrum toward red, the wavelengths are longer and have lower
energy ([link]).
Longer wavelength
vewow \/\S\/\/\S
aw AV AU AC AVAU AC
AV AC AVAVAUAUAUA
VIOLET FAVAVAVAVAVAVAVAVAVAT Shorter wavelength
More energy
Less energy
The colors of visible light do not carry the same amount of energy.
Violet has the shortest wavelength and therefore carries the most
energy, whereas red has the longest wavelength and carries the least
amount of energy. (credit: modification of work by NASA)
Understanding Pigments
Different kinds of pigments exist, and each has evolved to absorb only
certain wavelengths (colors) of visible light. Pigments reflect or transmit the
wavelengths they cannot absorb, making them appear in the corresponding
color.
Chlorophylls and carotenoids are the two major classes of photosynthetic
pigments found in plants and algae; each class has multiple types of
pigment molecules. There are five major chlorophylls: a, b, c and d anda
related molecule found in prokaryotes called bacteriochlorophyll.
Chlorophyll a and chlorophyll b are found in higher plant chloroplasts and
will be the focus of the following discussion.
With dozens of different forms, carotenoids are a much larger group of
pigments. The carotenoids found in fruit—such as the red of tomato
(lycopene), the yellow of corn seeds (zeaxanthin), or the orange of an
orange peel ((-carotene)—are used as advertisements to attract seed
dispersers. In photosynthesis, carotenoids function as photosynthetic
pigments that are very efficient molecules for the disposal of excess energy.
When a leaf is exposed to full sun, the light-dependent reactions are
required to process an enormous amount of energy; if that energy is not
handled properly, it can do significant damage. Therefore, many carotenoids
reside in the thylakoid membrane, absorb excess energy, and safely
dissipate that energy as heat.
Each type of pigment can be identified by the specific pattern of
wavelengths it absorbs from visible light, which is the absorption spectrum.
The graph in [link] shows the absorption spectra for chlorophyll a,
chlorophyll b, and a type of carotenoid pigment called B-carotene (which
absorbs blue and green light). Notice how each pigment has a distinct set of
peaks and troughs, revealing a highly specific pattern of absorption.
Chlorophyll a absorbs wavelengths from either end of the visible spectrum
(blue and red), but not green. Because green is reflected or transmitted,
chlorophyll appears green. Carotenoids absorb in the short-wavelength blue
region, and reflect the longer yellow, red, and orange wavelengths.
Absorption Spectra
Tet ae
Absorption of light
inn even SO ne
-
: &
1
See Se CONN Oaw~ 350 400 450 500 550 600 650
Wavelength (nm)
(c)
(a) Chlorophyll a, (b) chlorophyll b, and (c) B-carotene are
hydrophobic organic pigments found in the thylakoid
membrane. Chlorophyll a and b, which are identical except for
the part indicated in the red box, are responsible for the green
color of leaves. B-carotene is responsible for the orange color
in carrots. Each pigment has (d) a unique absorbance spectrum.
Many photosynthetic organisms have a mixture of pigments; using them,
the organism can absorb energy from a wider range of wavelengths. Not all
photosynthetic organisms have full access to sunlight. Some organisms
grow underwater where light intensity and quality decrease and change with
depth. Other organisms grow in competition for light. Plants on the
rainforest floor must be able to absorb any bit of light that comes through,
because the taller trees absorb most of the sunlight and scatter the
remaining solar radiation ([link]).
Plants that commonly grow in the shade
have adapted to low levels of light by
changing the relative concentrations of
their chlorophyll pigments. (credit: Jason
Hollinger)
When studying a photosynthetic organism, scientists can determine the
types of pigments present by generating absorption spectra. An instrument
called a spectrophotometer can differentiate which wavelengths of light a
substance can absorb. Spectrophotometers measure transmitted light and
compute from it the absorption. By extracting pigments from leaves and
placing these samples into a spectrophotometer, scientists can identify
which wavelengths of light an organism can absorb. Additional methods for
the identification of plant pigments include various types of
chromatography that separate the pigments by their relative affinities to
solid and mobile phases.
How Light-Dependent Reactions Work
The overall function of light-dependent reactions is to convert solar energy
into chemical energy in the form of NADPH and ATP. This chemical
energy supports the Calvin cycle and fuels the assembly of sugar molecules.
The light-dependent reactions are depicted in [link]. Protein complexes and
pigment molecules work together to produce NADPH and ATP.
(a) Photosystem II (P680)
Stroma
; Reaction Primary Light
Pigment center electron
molecules acceptor
Thylakoid
membrane
(b) Photosystem | (P700)
Light
A photosystem consists of a light-
harvesting complex and a reaction
center. Pigments in the light-
harvesting complex pass light
energy to two special chlorophyll
a molecules in the reaction center.
The light excites an electron from
the chlorophyll a pair, which
passes to the primary electron
acceptor. The excited electron
must then be replaced. In (a)
photosystem II, the electron comes
from the splitting of water, which
releases oxygen as a waste
product. In (b) photosystem I, the
electron comes from the
chloroplast electron transport
chain discussed below.
The actual step that converts light energy into chemical energy takes place
in a multiprotein complex called a photosystem [link], two types of which
are found embedded in the thylakoid membrane, photosystem IT (PSII) and
photosystem I (PSI) ((link]). The two complexes differ on the basis of what
they oxidize (that is, the source of the low-energy electron supply) and what
they reduce (the place to which they deliver their energized electrons).
Both photosystems have the same basic structure; a number of antenna
proteins to which the chlorophyll molecules are bound surround the
reaction center where the photochemistry takes place. Each photosystem is
serviced by the light-harvesting complex, which passes energy from
sunlight to the reaction center; it consists of multiple antenna proteins that
contain a mixture of 300—400 chlorophyll a and b molecules as well as
other pigments like carotenoids. The absorption of a single photon or
distinct quantity or “packet” of light by any of the chlorophylls pushes that
molecule into an excited state. In short, the light energy has now been
captured by biological molecules but is not stored in any useful form yet.
The energy is transferred from chlorophyll to chlorophyll until eventually
(after about a millionth of a second), it is delivered to the reaction center.
Up to this point, only energy has been transferred between molecules, not
electrons.
Electron
Stroma transport chain
Light "y+ yt Light
NADP*+H* NADPH
In the photosystem II (PSII) reaction center,
energy from sunlight is used to extract electrons
from water. The electrons travel through the
chloroplast electron transport chain to
photosystem I (PSI), which reduces NADP" to
NADPH. The electron transport chain moves
protons across the thylakoid membrane into the
lumen. At the same time, splitting of water adds
protons to the lumen, and reduction of NADPH
removes protons from the stroma. The net result is
a low pH in the thylakoid lumen, and a high pH in
the stroma. ATP synthase uses this
electrochemical gradient to make ATP.
The reaction center contains a pair of chlorophyll a molecules with a
special property. Those two chlorophylls can undergo oxidation upon
excitation; they can actually give up an electron in a process called a
photoact. It is at this step in the reaction center, this step in photosynthesis,
that light energy is converted into an excited electron. All of the subsequent
steps involve getting that electron onto the electron carrier NADP* for
delivery to the Calvin cycle where the electron is deposited onto carbon for
long-term storage in the form of a carbohydrate. PSII and PSI are two major
components of the photosynthetic electron transport chain, which also
includes the cytochrome complex, a group of reversibly oxidizable and
reducible proteins that forms part of the electron transport chain between
PSII and PSI.
The reaction center of PSII (called P680) delivers its high-energy electrons,
one at a time, to a Series of proteins and electron carriers (or primary
electron acceptors, which are pigments or other organic molecules in the
reaction center that accept energized electrons from the reaction center) that
sits between it and PSI. P680’s missing electron is replaced by extracting a
low-energy electron from water; thus, water is split and PSII is re-reduced
after every photoact. Splitting one HO molecule releases two electrons,
two hydrogen atoms, and one atom of oxygen. Splitting two molecules is
required to form one molecule of diatomic O, gas. About 10 percent of the
oxygen is used by mitochondria in the leaf to support oxidative
phosphorylation. The remainder escapes to the atmosphere where it is used
by aerobic organisms to support respiration.
As electrons move through the proteins that reside between PSII and PSI,
they lose energy. That energy is used to move hydrogen atoms from the
stromal side of the membrane to the thylakoid lumen. Those hydrogen
atoms, plus the ones produced by splitting water, accumulate in the
thylakoid lumen and will be used synthesize ATP in a later step. Because
the electrons have lost energy prior to their arrival at PSI, they must be re-
energized by PSI, hence, another photon is absorbed by the PSI antenna.
That energy is relayed to the PSI reaction center (called P700). P700 is
oxidized and sends a high-energy electron to NADP" to form NADPH.
Thus, PSII captures the energy to make ATP, and PSI captures the energy to
reduce NADP” into NADPH. The two photosystems work in concert, in
part, to guarantee that the production of NADPH will roughly equal the
production of ATP. Other mechanisms exist to fine tune that ratio to exactly
match the chloroplast’s constantly changing energy needs.
Generating an Energy Carrier: ATP
Chemiosmosis
In chemiosmosis, the free energy from the series of redox reactions just
described is used to pump hydrogen ions (protons) across the membrane.
The uneven distribution of H* ions across the thylakoid membrane
establishes both concentration and electrical gradients (thus, an
electrochemical gradient), owing to the hydrogen ions’ positive charge and
their aggregation on one side of the membrane.
If the thylakoid membrane were open to diffusion by the hydrogen ions, the
ions would tend to diffuse back across into the matrix, driven by their
electrochemical gradient. Recall that many ions cannot diffuse through the
nonpolar regions of phospholipid membranes without the aid of ion
channels. Similarly, hydrogen ions in the thylakoid lumen can only pass
through the thylakoid membrane through an integral membrane protein
called ATP synthase ([link]). This complex protein acts as a tiny generator,
turned by the force of the hydrogen ions diffusing through it, down their
electrochemical gradient. The turning parts of this molecular machine
facilitates the addition of a phosphate to ADP, forming ATP, using the
potential energy of the hydrogen ion gradient.
Thylakeid
Membrane
Stroma
ATP synthase is a complex,
molecular machine that uses a
proton (H*) gradient to form ATP
from ADP and inorganic
phosphate (Pi). (Credit:
modification of work by Klaus
Hoffmeier)
As a review, the buildup of hydrogen ions inside the thylakoid lumen
creates a concentration gradient. The passive diffusion of hydrogen ions
from high concentration (in the thylakoid lumen) to low concentration (in
the stroma) is harnessed to create ATP. The ions build up energy because of
diffusion and because they all have the same electrical charge, repelling
each other. To release this energy, hydrogen ions will rush through any
opening, similar to water jetting through a hole in a dam. In the thylakoid,
that opening is a passage through a specialized protein channel called the
ATP synthase. The energy released by the hydrogen ion stream allows ATP
synthase to attach a third phosphate group to ADP, which forms a molecule
of ATP ({link]). The flow of hydrogen ions through ATP synthase is called
chemiosmosis because the ions move from an area of high to an area of low
concentration through a semi-permeable structure.
Overview of Light-Dependent Reaction
Light energy is harvested and transformed into short term chemical energy
during the light-dependent reactions. The pigments in the reaction center of
photosytem II absorb light energy and excite electrons into the electron
transport chain. To replace the electrons excited in photosystem II, water is
spilt releasing electrons, H* ions and oxygen gas. As the electrons move
through the electron transport chain, energy, release by the movement of
electrons, is used to produce a H" ion gradient inside the thylakoid. The
process of chemiosmosis uses the H* concentration to produce ATP. After
flowing through the electron transport chain, the electrons enter
photosystem I. The reaction center of photosystem I absorbs more light
energy and excites electrons. These energized electrons reduce NADP” to
NADPH. See ([link])below for a visual representation of the light-
dependent reactions.
Light-Dependent
Reactions
Thylakoid
membrane
This is an image of the Light-Dependent Reactions of photosynthesis.
(Image by Eva Horne and Robert Bear)
Calvin Cycle
"By blending water and minerals from below with sunlight and CO, from
above, green plants link the earth to the sky. We tend to believe that plants
grow out of the soil, but in fact most of their substance comes from the air."
Fritjof Capra, The Web of Life: A New Scientific Understanding of Living
Systems, (1997)
After the energy from the sun is converted into chemical energy and
temporarily stored in ATP and NADPH molecules, the cell has the fuel
needed to build carbohydrate molecules for long-term energy storage. The
products of the light-dependent reactions, ATP and NADPH, have lifespans
in the range of millionths of seconds, whereas the products of the light-
independent reactions (carbohydrates and other forms of reduced carbon)
can survive for hundreds of millions of years. Carbohydrates, like the
cellulose that makes up the bulk of most plants, obviously contain carbon.
Where does the carbon come from? It comes from the air, in the form of
carbon dioxide, the gas that is a waste product of respiration in microbes,
fungi, plants, and animals.
The Calvin Cycle
In plants, carbon dioxide (CO>) enters the leaves through stomata, where it
diffuses over short distances through intercellular spaces until it reaches the
mesophyll cells. Once in the mesophyll cells, CO> diffuses into the stroma
of the chloroplast—the site of light-independent reactions of
photosynthesis. These reactions actually have several names associated with
them. Another term, the Calvin cycle, is named for the man who discovered
it, and because these reactions function as a cycle. Others call it the Calvin-
Benson cycle to include the name of another scientist involved in its
discovery. The most outdated name is dark reactions (the term originally
used by Melvin Calvin, who got the Nobel Prize for elucidating these
reactions), because light is not directly required ([link]). However, the term
dark reactions can be misleading because it implies incorrectly that the
reaction only occurs at night or is independent of light, which is why it has
faded from everyday usage.
Chloroplast
Light reactions harness energy from the sun to produce
chemical bonds, ATP, and NADPH. These energy-carrying
molecules are made in the stroma where carbon fixation takes
place. Work by Eva Horne and Robert A. Bear
The light-independent reactions of the Calvin cycle can be organized into
three basic stages: fixation, reduction, and regeneration.
Stage 1: Fixation
In the stroma, in addition to CO», two other components are present to
initiate the light-independent reactions: an enzyme called ribulose
bisphosphate carboxylase (RuBisCO), and three molecules of ribulose
bisphosphate (RuUBP), as shown in [link]. RuBP has five atoms of carbon,
flanked by two phosphates.
1/2 molecule glucose (CgH;20¢)
The Calvin cycle has three stages. In stage 1, the
enzyme RuBisCO incorporates carbon dioxide into
an organic molecule, PGA. In stage 2, the organic
molecule is reduced using electrons supplied by
NADPH. In stage 3, RuBP, the molecule that starts
the cycle, is regenerated so that the cycle can
continue. Only one carbon dioxide molecule is
incorporated at a time, so the cycle must be
completed three times to produce a single three-
carbon PGAL molecule, and six times to produce a
six-carbon glucose molecule. (Original by
OpenStax Modified by Robert A. Bear)
RuBisCO catalyzes a reaction between CO» and RuBP. For each CO»
molecule that reacts with one RuBP, two molecules of phosphoglycerate
(PGA) form. PGA has three carbons and one phosphate. Each turn of the
cycle involves only one RuBP and one carbon dioxide and forms two
molecules of PGA. The number of carbon atoms remains the same, as the
atoms move to form new bonds during the reactions (3 atoms from 3CO, +
15 atoms from 3RuBP = 18 atoms in 3 atoms of PGA). This process is
called carbon fixation, because CO, is “fixed” from an inorganic form into
organic molecules.
Stage 2: Reduction
ATP and NADPH are used to convert the six molecules of PGA into six
molecules of a chemical called phosphoglyceraldehyde (PGAL). That is a
reduction reaction because it involves the gain of electrons (from NADPH)
by PGA. Recall that a reduction is the gain of an electron by an atom or
molecule. Six molecules of both ATP and NADPH are used; making
glucose is obviously an energy-intensive activity. For ATP, energy is
released with the loss of the terminal phosphate atom, converting it into
ADP; for NADPH, both energy and a hydrogen atom are lost, converting it
into NADP". Both of these molecules return to the nearby site of the light-
dependent reactions to be reused and re-energized.
Stage 3: Regeneration
Interestingly, at this point, only one of the PGAL molecules leaves the
Calvin cycle and is sent to the cytoplasm to contribute to the formation of
other compounds needed by the plant. Because the PGAL exported from
the chloroplast has three carbon atoms, it takes three “turns” of the Calvin
cycle to fix enough net carbon to export one PGAL. But each turn makes
two PGAL, thus three turns make six PGAL. One is exported while the
remaining five PGAL molecules remain in the cycle and are used to
regenerate RuBP, which enables the system to prepare for more CO, to be
fixed. Three more molecules of ATP are used in these regeneration
reactions.
Overview of Calvin Cycle
During the Calvin cycle, energy and electrons harvested in the light-
dependent reactions are used to produce carbohydrates i.e. glucose. There
are three stages in the Calvin cycle. The first stage is carbon fixation, CO
from the atmosphere is attached to an organic molecule RuBP during this
stage. The second stage is the carbon reduction, the energy and electrons in
ATP and NADPH are used to produce carbohydrates (glucose). The last
Stage is the regeneration stage, energy from ATP is used to regenerate the
first substrate of the cycle (RUBP). See ({link]) below for a review of the
Calvin Cycle.
Calvin Cycle —
This image represents the Calvin Cycle. (Image by Eva Home and
Robert Bear)
Note:
Evolution Connection
Photosynthesis
During the evolution of photosynthesis, a major shift occurred from the
bacterial type of photosynthesis that involves only one photosystem and is
typically anoxygenic (does not generate oxygen) into modern oxygenic
(does generate oxygen) photosynthesis, employing two photosystems. This
modern oxygenic photosynthesis is used by many organisms—from giant
tropical leaves in the rainforest to tiny cyanobacterial cells—and the
process and components of this photosynthesis remain largely the same.
Photosystems absorb light and use electron transport chains to convert
energy into the chemical energy of ATP and NADH. The subsequent light-
independent reactions then assemble carbohydrate molecules with this
energy.
Photosynthesis in desert plants has evolved adaptations that conserve
water. In the harsh dry heat, every drop of water must be used to survive.
Because stomata must open to allow for the uptake of CO>, water escapes
from the leaf during active photosynthesis. Desert plants have evolved
processes to conserve water and deal with harsh conditions. A more
efficient use of CO> allows plants to adapt to living with less water. Some
plants such as cacti ({link]) can prepare materials for photosynthesis during
the night by a temporary carbon fixation/storage process, because opening
the stomata at this time conserves water due to cooler temperatures. In
addition, cacti have evolved the ability to carry out low levels of
photosynthesis without opening stomata at all, an extreme mechanism to
face extremely dry periods.
The harsh conditions of the desert have led plants
like these cacti to evolve variations of the light-
independent reactions of photosynthesis. These
variations increase the efficiency of water usage,
helping to conserve water and energy. (credit:
David A. Rintoul)
Overview of Photosynthesis
Photosynthesis converts light energy to chemical energy in two stages, the
light-dependent reactions and the Calvin cycle. By exploring these two sets
of reactions, we learned how photons of light energy are turned into food by
photosynthesis. The light-dependent reactions harvest the light energy to
make ATP and to transfer electrons from H»O to NADP" forming NADPH
and Oxygen gas. The energy and electrons in ATP and NADPH are used in
the Calvin cycle to produce glucose from carbon dioxide. The sunlight
energy entering the chloroplasts becomes stored as the chemical bonds in
the organic molecules. See ({link]) below for a review of photosynthesis.
eed
The process of photosynthesis is divided to two stages
that are linked by the energy and electron carriers ATP
and NADPH. The light-dependent reactions split water
and releases oxygen as a byproduct, and these reactions
convert light energy to chemical energy (ATP and
NADPH). The Calvin cycle uses the energy in ATP and
NADPH and produces carbohydrates by fixing CO, a
byproduct of aerobic cellular respiration. (Image by Eva
Horne and Robert Bear)
What is the fate of the carbohydrates produced by photosynthesis? About
50% of the carbohydrates are used by the plant for aerobic cellular
respiration in their mitochondria. The other 50% of the carbohydrates are
the building blocks for the biological macromolecules the make up plant
cells that you learned about in module 3. As you may realize, these
biological macromolecules are the food we eat, and you are what you eat.
Taking this a bit further, all the activities you do from reading this text to
sleeping require energy and that energy comes from the Sun.
Overview of Cellular Respiration
This is a general overview of cellular respiration.
Introduction
"Surely the mitochondrion that first entered another cell was not thinking
about the future benefits of cooperation and integration; it was merely
trying to make its own living in a tough Darwinian world." Stephen Jay
Gould, in Wonderful Life: the Burgess Shale and the Nature of History,
(1990)
All living organisms require energy, and for all organisms this energy
comes from the chemical energy found in compounds that they acquire
from their environment. The mitochondrion, a descendent of an aerobically-
respiring bacteria, is the site of energy generation in eukaryotes. As we
learned previously, the process of photosynthesis uses solar energy
(sunlight) and converts this energy into chemical energy in the form of
carbohydrates. In order for the chemical energy in the carbohydrates to be
made available to do cellular work, the energy must be converted into a
useable form known as ATP. Adenosine Triphosphate is the energy currency
of the cell, and everything you do from walking down the street to reading
this book requires energy in the form of ATP. Organisms need a constant
supply of ATP, and the potential energy stored in food is the source of
energy to meet this need. By connecting all this together, you should realize
that your daily activities are fueled by the energy from the sun and that even
on the cellular level nutrients cycle and energy flows ([link]).
This image illustrates the relationship between
photosynthesis and cellular respiration. (Image by Eva
Horne and Robert Bear)
All organisms need ATP, but not all organisms use the same pathways to
generate ATP from the food that is consumed. Aerobic cellular
respiration, the main subject of this chapter, uses oxygen (O>) and glucose
to generate ATP. Organisms (plants, animals, fungi and microbes) that live
in an oxygen (O>) rich environment use this process to generate ATP. The
overall equation for aerobic cellular respiration is the reverse of
photosynthesis, is an exergonic reaction, and supplies the ATP for cellular
functions ([Link]).
Aerobic Cellular Respiration
Energy
Carbon
———————>
Glucose + Oxygen ATP + Dioxide * Water
This image illustrates the overall equation for
aerobic cellular respiration and how the amounts of
free energy differs between the reactants and the
products. (Image by Robert Bear)
As the aerobic cellular respiration equation shows ([link]), an organism
needs to acquire the O> from its surroundings and to get rid of the CO, that
is produced. The acquisition of O» and the release of CO, is accomplished
in a variety of ways. In single celled organisms, the movement of O» and
CO> (gas exchange) is done by simple diffusion. However, in complex
organisms there are specialized organs that allow for gas exchange; for
example, gills in aquatic organisms and lungs in terrestrial animals.
A common misconception is that plants do not undergo cellular respiration
because they make their own energy by photosynthesis. Plants do perform
cellular respiration using the carbohydrates produced via photosynthesis;
this occurs in tissues that are not photosynthetically active (e.g., roots), as
well as in leaves and stems. Approximately half of the glucose produced by
photosynthesis is consumed by the plant, mostly to generate ATP during
aerobic cellular respiration. Other uses of glucose in the plant include
synthesis of cell walls, starch, and other plant carbohydrates. So, plants
harvest light energy via photosynthesis, making carbohydrates, and then
they use the energy stored in those carbohydrates to perform various
cellular functions. This is the reason why they are called autotrophs, or self
feeders.
Some single-celled organisms use anaerobic metabolism to extract energy
from biological molecules; this process occurs in the absence of oxygen. In
this chapter, we will explore one type of anaerobic metabolism called
fermentation. You may already be familiar with a one type of fermentation,
lactic acid fermentation, especially if you have recently over-exerted your
muscles. Anaerobic metabolism is used by many organisms to produce ATP
when oxygen is not available and thus pathways which require oxygen
cannot be used. The amount of ATP produced by fermentation is much less
then that produced by aerobic cellular respiration, so there is a cost and
benefit associated with organisms utilizing fermentation.
Summary of Aerobic Cellular Respiration
Aerobic cellular respiration ([link]) is series of linked chemical reactions
that can be best understood if it is separated into four stages. These are
glycolysis, pyruvate oxidation, the Krebs Cycle, and oxidative
phosphorylation. Similar to photosynthesis, cellular respiration uses a
series of oxidation-reduction reactions. During these reactions, electrons are
stripped from the chemical bonds of the original glucose molecule and
eventually added to oxygen, via a series of intermediate steps. This series of
reactions releases small amounts of energy at each step; this energy is used
to drive the formation of ATP. This section is a brief introduction to the
stages of aerobic respiration with more detail to follow in the chapter.
Cytoplasm Caos
ATP
Oxidative
Phosphory-
lation
Aerobic Cellular Respiration
This image illustrates aerobic cellular respiration. (Image by Eva
Horne and Robert Bear)
The first stage of cellular respiration is called Glycolysis and occurs in the
cytoplasm of the cell. During glycolysis, 1 glucose molecule (with 6 carbon
atoms) is broken down into 2 pyruvate molecules (with three carbon atoms
each). This is accompanied by the production of a few ATP molecules and
the storage of some high-energy electrons on the electron carrier NADH.
Note that no O> is needed for this set of reactions, which means that
glycolysis can proceed in the absence of oxygen.
The second stage is a short series of reactions called the oxidation of
pyruvate during which pyruvate (3 carbon atoms) is converted to acetyl-
CoA (two carbon atoms), accompanied by the production of CO» (one
carbon atom). This process occurs on the mitochondrial inner membrane,
and as a result the acetyl-CoA is formed inside the mitochondria. Pyruvate
is made in the cytoplasm, and this step moves the next compound in the
pathway into the mitochodria. This is critical, since all subsequent steps in
the pathway occur within the mitochondria. The other important event of
this stage is the addition of high-energy electrons to NAD", generating
another molecule of the electron carrier NADH.
Acetyl-CoA enters into the Krebs cycle, a series of mitochondrial reactions
that completes the breakdown of the original glucose, thereby releasing
CO>. In this third stage of the process, energy is harvested in the form of
high-energy electrons being used to generate NADH as well as another
high-energy electron carrier, FADHp. The reactions of the Krebs cycle also
produce a small amount of ATP.
So far, a minimal amount of ATP has been produced, but a lot of energy has
been stored in the electron carriers NADH and FADH). In the final stage of
aerobic cellular respiration, Oxidative Phosphorylation, a series of
enzymes known as the electron transport chain uses those high-energy
electrons to produce a large amount of ATP. The high energy electrons
harvested in the first three stages, and ferried by electron carriers (NADH
and FADH,) to the electron transport chain, are used to produce large
amounts of ATP vir the mitochondrial membrane protein known as the ATP
synthase. During this final stage is also when atmospheric oxygen is used
as the final electron and hydrogen ion acceptor, in a reaction which
produces water. The need for O> in this final step means that these reactions
are part of aerobic cellular respiration.
Location and Structures of Aerobic Cellular Respiration
All eukaryotic cells (protists, fungi, plants and animals) have mitochondria,
and mitochondria are often called the power plants of the cell because these
organelles produce a large amount of ATP. As you may remember from a
previous module, the mitochondrion is an organelle that is hypothesized to
have originated as an endosymbiotic aerobic bacteria. Some of the evidence
for this hypothesis comes from the relationship of the functional parts of the
mitochondria (({link]) to the structure of a typical aerobic bacteria. There is
an outer membrane which defines the organelle and represents the
membrane which enveloped the bacteria when it was taken into the cell via
endocytosis. The inner membrane represents the plasma membrane of the
bacteria; the inner and outer membranes together form the intermembrane
space. The inner membrane is highly folded; these folds are called
cristae. The extensive folding increases the surface area for the numerous
electron transport chain enzymes and the ATP synthases that are used to
make ATP. In bacteria all of these enzymes are packed into the plasma
membrane, as one would expect if the endosymbiotic hypothesis is correct.
The production of ATP is driven by a concentration gradient between the
outer and inner compartment; in aerobic bacteria this concentration gradient
is between the inside and the outside of the cell. The innermost
compartment, derived from the cytoplasm of the ancestral bacteria, is called
the matrix, and this compartment (just like the cytoplasm of today's
bacteria) contains ribosomes and DNA; It is also the location of the Krebs
Cycle reactions.
Intermembrane space Inner Membrane
HAAN
Outer Membrane Matrix
This image illustrates the structures within the mitochondria. (Image
by Eva Horne and Robert Bear)
Glycolysis
Introduction
"My main thesis will be that in the study of the intermediate processes of
metabolism we have to deal not with complex substances which elude
ordinary chemical methods, but with the simple substances undergoing
comprehensible reactions." Sir Frederick Gowland Hopkins, 1933
You have read that nearly all of the energy used by living cells comes to
them in the bonds of the simple 6-carbon sugar, glucose. Glycolysis
(literally "sugar splitting") is the first step in the breakdown of glucose to
extract energy for cellular metabolism. Nearly all living organisms carry out
glycolysis as part of their metabolism. The process does not use oxygen and
is therefore anaerobic. Glycolysis takes place in the cytoplasm of both
prokaryotic and eukaryotic cells.
Glycolysis begins with the six carbon ring-shaped structure of a single
glucose molecule and ends with two molecules of a three-carbon sugar
called pyruvate. Glycolysis consists of two distinct phases. The first part of
the glycolysis pathway traps the glucose molecule in the cell and uses
energy to modify it so that the six-carbon sugar molecule can be split
evenly into the two three-carbon molecules. The second part of glycolysis
extracts energy from the chemical bonds in the molecules and stores it in
the form of ATP and NADH, the reduced form of NAD.
First Half of Glycolysis (Energy-Requiring Steps)
Step 1. The first step in glycolysis ([link]) is catalyzed by hexokinase, an
enzyme with broad specificity that catalyzes the phosphorylation (addition
of a phosphate molecule) of six-carbon sugars. Hexokinase phosphorylates
glucose using ATP as the source of the phosphate, producing glucose-6-
phosphate, a more high-energy form of glucose. This reaction prevents the
phosphorylated glucose molecule from being transported out of the cell via
glucose transporters in the plasma memrane. It can no longer leave the cell
because the transport proteins recognize unmodified glucose, but not the
phosphorylated version.
Step 2. In the second step of glycolysis, an isomerase converts glucose-6-
phosphate into one of its isomers, fructose-6-phosphate. An isomerase is an
enzyme that catalyzes the conversion of a molecule into one of its isomers
(compounds with the same numbers and kinds of atoms arranged in
different configurations). This change from phosphoglucose to
phosphofructose facilitates the eventual split of the sugar into two three-
carbon molecules.
Step 3. The third step is the phosphorylation of fructose-6-phosphate,
catalyzed by the enzyme phosphofructokinase. A second ATP molecule
donates a high-energy phosphate to fructose-6-phosphate, producing
fructose-1,6-bisphosphate. In this pathway, phosphofructokinase is a rate-
limiting enzyme. It is active when the concentration of ADP is high; it is
less active when ADP levels are low and the concentration of ATP is high.
Thus, if there is “sufficient” ATP in the system, the pathway slows down.
This is a type of end product inhibition, since ATP is the end product of
glucose catabolism.
Step 4. The newly added high-energy phosphate further destabilizes
fructose-1,6-bisphosphate, which is now a very high-energy compound. The
fourth step in glycolysis employs an enzyme, aldolase, to cleave fructose-
1,6-bisphosphate into two phosphorylated three-carbon isomers:
dihydroxyacetone-phosphate and glyceraldehyde-3-phosphate.
Step 5. In the fifth step, an isomerase transforms the dihydroxyacetone-
phosphate into its isomer, glyceraldehyde-3-phosphate. Thus, the pathway
will continue with two molecules of a single isomer. At this point in the
pathway, there is a net investment of energy from two ATP molecules in the
breakdown of one glucose molecule.
WY
@ 2 @ @ f-0-420
H C20 O
A H (e) a P
H H-C=0 H-C-OH He=O=hIO HO-C=H —_ Dihydroxyacetone-
HeCeOH ATP = ADP -C-OH c2o ATP ADP 414} phosphate
' ' =
CH-O HOsC
H
H HO-C-H
H / NY ie oe : en HO-CH Fructose Triose
Cc Cc i > = en bisphosphate hosphate (5)
HO” Ne iv Non Hexokinase H-C-OH _ Phosphoglucose Hee _ Phosphofructo- H Cc ‘OH aldose P pipiens
C=C 1” 9 isomerase 1 9 kinase H=C-OH 07
'
H OH H-G-O-Ps0 HG Osea H-¢-0-P=0 "
H fo H o 4 § 7 ¢=0
fe asec H=C*OH g- Glyceraldehyde-
Glucose Glucose-6-phosphate Fructose-6-phosphate Fructose-1,6-biphosphate i ‘ _o-b2o 3-phosphate
A ¢&
The first half of glycolysis uses two ATP molecules in the
phosphorylation of glucose, which is then split into two three-carbon
molecules.
Second Half of Glycolysis (Energy-Releasing Steps)
So far, glycolysis has cost the cell two ATP molecules and produced two
small, three-carbon sugar molecules. Both of these molecules will proceed
through the second half of the pathway, and sufficient energy will be
extracted to pay back the two ATP molecules used as an initial investment
and produce a profit for the cell of two additional ATP molecules and two
even higher-energy NADH molecules.
Step 6. The sixth step in glycolysis ({link]) oxidizes the sugar
(glyceraldehyde-3-phosphate), extracting high-energy electrons, which are
picked up by the electron carrier NAD*, producing NADH. The sugar is
then phosphorylated by the addition of a second phosphate group,
producing 1,3-bisphosphoglycerate. Note that the addition of a second
phosphate group does not require another high-energy ATP molecule;
inorganic phosphate ions in the cytoplasm are used instead.
0
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Pyruvate fe a 2-Phosphoglycerate 3-Phosphoglycerate 1,3-Bisphosphoglycerate
The second half of glycolysis involves phosphorylation without ATP
investment (step 6) and produces two NADH and four ATP
molecules per glucose.
Here again is a potential limiting factor for this pathway. The continuation
of the reaction depends upon the availability of the oxidized form of the
electron carrier, NAD*. Thus, NADH must be continuously oxidized back
into NAD" in order to keep this step going. If NAD* is not available, the
second half of glycolysis slows down or stops. If oxygen is available in the
system, the NADH will be oxidized readily, though indirectly, and the high-
energy electrons from the hydrogen released in this process will be used to
produce ATP. In an environment without oxygen, an alternate pathway
(fermentation) can provide the oxidation of NADH to NAD".
Step 7. In the seventh step, catalyzed by phosphoglycerate kinase (an
enzyme named for the reverse reaction), 1,3-bisphosphoglycerate donates a
high-energy phosphate to ADP, forming one molecule of ATP. This is an
example of substrate-level phosphorylation, where a phosphate group is
added to ADP by removing it from another compound rather than from the
phosphate ions in the cytoplasm.. A carbonyl group on the 1,3-
bisphosphoglycerate is oxidized to a carboxyl group, and 3-
phosphoglycerate is formed.
Step 8. In the eighth step, the remaining phosphate group in 3-
phosphoglycerate moves from the third carbon to the second carbon,
producing 2-phosphoglycerate (an isomer of 3-phosphoglycerate). The
enzyme catalyzing this step is a mutase (isomerase).
Step 9. An enzyme called enolase catalyzes the ninth step. This enzyme
causes 2-phosphoglycerate to lose water from its structure; this is a
condensation reaction, resulting in the formation of a double bond that
increases the potential energy in the remaining phosphate bond and
produces phosphoenolpyruvate (PEP).
Step 10. The last step in glycolysis is catalyzed by the enzyme pyruvate
kinase (the enzyme in this case is named for the reverse reaction of
pyruvate’s conversion into PEP) and results in the production of a second
ATP molecule by substrate-level phosphorylation and the compound
pyruvic acid (or its salt form, pyruvate). Many enzymes in enzymatic
pathways are named for the reverse reactions, since the enzyme can
catalyze both forward and reverse reactions (these may have been described
initially by the reverse reaction that takes place in vitro, under non-
physiological conditions).
Outcomes of Glycolysis
Glycolysis starts with glucose and produces two pyruvate molecules, a total
of four ATP molecules and two molecules of NADH ([link]). Two ATP
molecules were used in the first half of the pathway to prepare the six-
carbon ring for cleavage, so the cell has a net gain of two pyruvate
molecules, two ATP molecules and 2 NADH molecules for its use. If the
cell cannot catabolize the pyruvate molecules further, it will harvest only
these two ATP molecules from one molecule of glucose. For example,
mature mammalian red blood cells are not capable of aerobic cellular
respiration (they have no mitochondria), so glycolysis is their sole source of
ATP.
Cytoplasm
Glycolysis
This image is an overview of glycolysis which occurs in the
cytoplasm of a cell. Glucose is catabolized into 2 pyruvate molecules
with 2 NAD* reduced to 2 NADH. Two ATP molecules are
consumed, while 4 are produced, yielding a net gain of 2 ATP
molecules. (Image by Eva Horne and Robert Bear
Oxidation of Pyruvate and the Krebs Cycle
"It is the destiny of wine to be drunk, and it is the destiny of glucose to be
oxidized. But it was not oxidized immediately: its drinker kept it in his liver
for more than a week, well curled up and tranquil, as a reserve aliment for a
sudden effort; an effort that he was forced to make the following Sunday,
pursuing a bolting horse. " Primo Levi, The Periodic Table, 1975
If oxygen is available, aerobic cellular respiration will go forward. In
eukaryotic cells, the pyruvate molecules produced at the end of glycolysis
are transported into mitochondria, which are the sites of aerobic cellular
respiration. There, pyruvate (three carbons) will be transformed into an
acetyl group (two carbons) that will be attached to a carrier compound
called coenzyme A (CoA). The resulting compound is called acetyl-CoA.
CoA is made from vitamin B5, pantothenic acid. Acetyl-CoA can be used
in a variety of ways by the cell, but its major function is to deliver the two-
carbon energy source derived from pyruvate to the next stage of the aerobic
cellular respiration pathway.
Oxidation of Pyruvate
In order for pyruvate, the product of glycolysis, to enter the next pathway, it
must undergo several changes. The conversion is a three-step process
({link]).
Oxidation of Pyruvate
NAD* NADH
ae
COE
Oxidation
reaction
A carboxyl group NAD* is reduced An acetyl group is
is removed from to NADH. transferred to
pyruvate, releasing coenzyme A,
carbon dioxide. resulting in acetyl -
CoA.
Upon entering the mitochondrial
matrix, a multi-enzyme complex
converts pyruvate into acetyl-CoA. In
the process, carbon dioxide is released
and one molecule of NADH is
formed.
Step 1. A carboxyl group is removed from pyruvate, releasing a molecule of
carbon dioxide into the surrounding medium. The result of this step is a
two-carbon hydroxyethyl group bound to the enzyme (pyruvate
dehydrogenase). This is the first of the six carbons from the original glucose
molecule to be removed. This step proceeds twice for each glucose
molecule (remember: there are two pyruvate molecules produced at the end
of glycolsis). Thus, two of the six carbons will have been removed at the
end of this step in aerobic cellular respiration.
Step 2. The hydroxyethyl group is oxidized to an acetyl group, and the
electrons are picked up by NAD”, forming NADH. The high-energy
electrons from NADH will be used later to generate ATP.
Step 3. The enzyme-bound acetyl group is transferred to CoA, producing a
molecule of acetyl-CoA.
During the oxidation of pyruvate, the incoming pyruvate is converted to
acetyl-CoA, NAD” is reduced to NADH and a carbon dioxide is released
for each pyruvate entering the stage ([Link]).
Cytoplasm Cinco
v
Oxidation of Pyruvate
This image is an overview of the oxidation of pyruvate. During this
stage, carbon dioxide is release, NAD™ is reduced to NADH and
acetyl-CoA is formed. (Image by Eva Horne and Robert Bear)
Krebs Cycle
In the presence of oxygen, the two carbons in acetyl-CoA are added to to a
four-carbon molecule, oxaloacetate, to form citrate (aka citric acid), a six-
carbon molecule. This is the starting point of the Krebs Cycle, which will
harvest the remainder of the extractable energy from what began as a
glucose molecule. This single pathway has several different names: the
citric acid cycle (for citric acid, the first compound in the cycle), the
tricarboxylic acid (TCA) cycle (since citric acid has 3 carboxyl groups, and
is thus a tricarboxylic acids), and the Krebs cycle, after Hans Krebs, who
first identified the steps in the pathway in the 1930s in pigeon flight
muscles. This work earned Krebs a share (with Fritz Lippman) of the 1953
Nobel Prize in Physiology and Medicine.
After the conversion of pyruvate to acetyl CoA by enzymes in the
mitochondrial inner membrane, the Krebs cycle takes place in the matrix of
mitochondria. Almost all of the enzymes of the Krebs cycle are soluble
(i.e., not bound to the membrane), with the single exception of the enzyme
succinate dehydrogenase, which is embedded in the inner membrane of the
mitochondrion. Unlike glycolysis, the Krebs cycle is a closed loop: The last
part of the pathway regenerates the compound (oxaloacetate) used in the
first step. The eight steps of the cycle are a series of redox, condensation,
hydrolysis, and decarboxylation reactions that produce two carbon dioxide
molecules, one GTP/ATP, and reduced forms of NADH and FADH>
({link]). Even though oxygen is not directly required for these reactions, this
is considered an aerobic pathway because the NADH and FADH) produced
must transfer their electrons to the next pathway in the system, which will
use oxygen. If this transfer does not occur, there won't be any NAD or
FADH regenerated, and the oxidation steps of the Krebs cycle cannot occur
without those oxidized electron carriers. Note that the Krebs cycle produces
very little ATP directly and does not directly consume oxygen.
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In the Krebs cycle, the acetyl group from acetyl CoA is
attached to a four-carbon oxaloacetate molecule to form
a six-carbon citrate molecule. Through a series of steps,
citrate is oxidized, releasing two carbon dioxide
molecules for each acetyl group fed into the cycle. In the
process, three NAD* molecules are reduced to NADH,
one FAD molecule is reduced to FADH, and one ATP or
GTP (depending on the cell type) is produced (by
substrate-level phosphorylation). Because the final
product of the citric acid cycle is also the first reactant,
the cycle runs continuously in the presence of sufficient
reactants. (credit: modification of work by
“Yikrazuul”/Wikimedia Commons)
Steps in the Krebs Cycle
Step 1. Prior to the start of the first step, a transitional phase occurs during
which pyruvic acid is converted to acetyl-CoA. Then, the first step of the
cycle begins: This is a condensation step, combining the two-carbon acetyl
group with a four-carbon oxaloacetate molecule to form a six-carbon
molecule of citrate. CoA is bound to a sulfhydryl group (-SH) and diffuses
away to eventually combine with another acetyl group. This step is
irreversible because it is highly exergonic. The rate of this reaction is
controlled by negative feedback and the amount of ATP available. If ATP
levels increase, the rate of this reaction decreases. If ATP is in short supply,
the rate increases.
Step 2. In step two, citrate loses one water molecule and gains another as
citrate is converted into its isomer, isocitrate.
Step 3. In step three, isocitrate is oxidized, producing a five-carbon
molecule, a-ketoglutarate, together with a molecule of CO, and two
electrons, which reduce NAD* to NADH. This step is also regulated by
negative feedback from ATP and NADH, and a positive effect of ADP.
Steps 3 and 4. Steps three and four are both oxidation and decarboxylation
steps, which release electrons that reduce NAD* to NADH and release
carboxyl groups that form CO, molecules. a-Ketoglutarate is the product of
step three, and a succinyl group is the product of step four. CoA binds the
succinyl group to form succinyl CoA. The enzyme that catalyzes step four
is regulated by feedback inhibition of ATP, succinyl CoA, and NADH.
Step 5. In step five, a phosphate group is substituted for coenzyme A, and a
high-energy bond is formed. This energy is used in substrate-level
phosphorylation (during the conversion of the succinyl group to succinate)
to form either guanine triphosphate (GTP) or ATP. There are two forms of
the enzyme, called isoenzymes, for this step, depending upon the type of
animal tissue in which they are found. One form is found in tissues that use
large amounts of ATP, such as heart and skeletal muscle. This form
produces ATP. The second form of the enzyme is found in tissues that have
a high number of anabolic pathways, such as liver. This form produces
GTP. GTP is energetically equivalent to ATP; however, its use is more
restricted. In particular, protein synthesis primarily uses GTP.
Step 6. Step six is a condensation reaction that converts succinate into
fumarate. Two hydrogen atoms are transferred to FAD, producing FADH).
The energy contained in the electrons of these atoms is insufficient to
reduce NAD* but adequate to reduce FAD. Unlike NADH, this carrier
remains attached to the enzyme and transfers the electrons to the electron
transport chain directly. This process is made possible by the localization of
the enzyme catalyzing this step inside the inner membrane of the
mitochondrion.
Step 7. Water is added to fumarate during step seven, and malate is
produced. The last step in the Krebs cycle regenerates oxaloacetate by
oxidizing malate. Another molecule of NADH is produced in the process.
Products of the Krebs Cycle
Two carbon atoms come into the Krebs cycle from each acetyl group,
representing four out of the six carbons of one glucose molecule. Two
carbon dioxide molecules are released on each turn of the cycle; however,
these do not necessarily contain the most recently added carbon atoms. The
two acetyl carbon atoms will eventually be released on later turns of the
cycle; thus, all six carbon atoms from the original glucose molecule are
eventually incorporated into carbon dioxide. Each turn of the cycle forms
three NADH molecules and one FADH> molecule. These carriers will
connect with the last portion of aerobic respiration to produce ATP
molecules. One ATP is also made in each cycle ([link]).
Glucose
Cytoplasm
V ATP.
Pyruvate
Acetyl-CoA
Krebs Cycle
This is an overview of the Krebs cycle. (Image by Eva Horne and
Robert Bear)
Oxidative Phosphorylation
Introduction
"Finally, to the theme of the respiratory chain, it is especially noteworthy
that David Keilin's chemically simple view of the respiratory chain appears
now to have been right all along — and he deserves great credit for having
been so reluctant to become involved when the energy-rich chemical
intermediates began to be so fashionable. This reminds me of the aphorism:
"the obscure we see eventually, the completely apparent takes longer.""
Peter D. Mitchell, Nobel Lecture 1978
Mitchell got the Nobel Prize for elucidating the details of one of the biggest
mysteries of life — How does the energy in NADH and FADH) get
converted to ATP. His explanation, now known as the chemiosmotic
hypothesis is quite simple in concept, and involves things you already
understand, like solute gradients across membranes and redox reactions.
You have just read about two pathways in glucose catabolism—glycolysis
and the Kreb's cycle cycle—that generate ATP. Most of the ATP generated
during the aerobic catabolism of glucose, however, is not generated directly
from these pathways. Rather, it is derived from a process that begins with
moving electrons through a series of electron transporters that undergo
redox reactions. This causes hydrogen ions to accumulate within the
intermembrane space. Therefore, a concentration gradient forms; this
concentration gradient represents potential energy. That energy is dissipated
when hydrogen ions diffuse back into the mitochondrial matrix, passing
through a channel formed by the ATP synthase embedded in the
membrane. As they flow through, the ATP synthase uses that energy to
make ATP, just like a water-powered generator uses water flow to generate
electricity. The current of hydrogen ions powers the catalytic action of ATP
synthase, which phosphorylates ADP, producing ATP.
Electron Transport Chain
The electron transport chain ((link]) is the last component of aerobic
cellular respiration and is the only part of glucose metabolism that uses
atmospheric oxygen. Oxygen continuously diffuses into plants and single-
celled organisms; in animals, it enters the body through the respiratory
system. Electron transport is a series of redox reactions that resemble a
relay race or bucket brigade; electrons are passed rapidly from one
component to the next, eventually arriving at the endpoint of the chain
where the electrons are used to reduce molecular oxygen, producing water.
There are four complexes composed of proteins, labeled I through IV in
[link], and the aggregation of these four complexes, together with
associated mobile, accessory electron carriers, is called the electron
transport chain. The electron transport chain is present in multiple copies in
the inner mitochondrial membrane of eukaryotes and the plasma membrane
of prokaryotes.
Electron Transport Chain
Intermembrane space
ae )/
i
Mir eer
Wi WV ECU EY
Mitochondrial matrix Inner mitochondrial membrane
The electron transport chain is a
series of electron transporters
embedded in the inner
mitochondrial membrane that
shuttles electrons from NADH and
FADH)> to molecular oxygen. In
the process, protons are pumped
from the mitochondrial matrix to
the intermembrane space, and
oxygen is reduced to form water.
Complex I
To start, two electrons are carried to the first complex aboard NADH. This
complex, labeled I, is composed of flavin mononucleotide (FMN) and an
iron-sulfur (Fe-S)-containing protein. FMN, which is derived from vitamin
Bo also called riboflavin, is one of several prosthetic groups or co-factors in
the electron transport chain. A prosthetic group is a non-protein molecule
required for the activity of a protein. Prosthetic groups are organic or
inorganic, non-peptide molecules bound to a protein that facilitate its
function; prosthetic groups include co-enzymes, which are the prosthetic
groups of enzymes. The enzyme in complex I is NADH dehydrogenase and
is a very large protein, containing 45 amino acid chains. Complex I can
pump four hydrogen ions across the membrane from the matrix into the
intermembrane space, and it is in this way that the hydrogen ion gradient is
established and maintained between the two compartments separated by the
inner mitochondrial membrane.
Q and Complex II
Complex II directly receives FADH), which does not pass through complex
I. The compound connecting the first and second complexes to the third is
ubiquinone (Q). The Q molecule is lipid soluble and freely moves through
the hydrophobic core of the membrane. Once it is reduced, (QH)),
ubiquinone delivers its electrons to the next complex in the electron
transport chain. Q receives the electrons derived from NADH from complex
I and the electrons derived from FADH) from complex II, including
succinate dehydrogenase. This enzyme and FADH> form a small complex
that delivers electrons directly to the electron transport chain, bypassing the
first complex. Since these electrons bypass and thus do not energize the
proton pump in the first complex, fewer ATP molecules are made from the
FADH) electrons. The number of ATP molecules ultimately obtained is
directly proportional to the number of protons pumped across the inner
mitochondrial membrane.
Complex III
The third complex is composed of cytochrome b, another Fe-S protein,
Rieske center (2Fe-2S center), and cytochrome c proteins; this complex is
also called cytochrome oxidoreductase. Cytochrome proteins have a
prosthetic group of heme. The heme molecule is similar to the heme in
hemoglobin, but it carries electrons, not oxygen. As a result, the iron ion at
its core is reduced and oxidized as it passes the electrons, fluctuating
between different oxidation states: Fe’* (reduced) and Fe*** (oxidized).
The heme molecules in the cytochromes have slightly different
characteristics due to the effects of the different proteins binding them,
giving slightly different characteristics to each complex. Complex III
pumps protons through the membrane and passes its electrons to
cytochrome c for transport to the fourth complex of proteins and enzymes
(cytochrome c is the acceptor of electrons from Q; however, whereas Q
carries pairs of electrons, cytochrome c can accept only one at a time).
Complex IV
The fourth complex is composed of cytochrome proteins c, a, and a3. This
complex contains two heme groups (one in each of the two cytochromes, a,
and a3) and three copper ions (a pair of Cu, and one Cup in cytochrome a3).
The cytochromes hold an oxygen molecule very tightly between the iron
and copper ions until the oxygen is completely reduced. The reduced
oxygen then picks up two hydrogen ions from the surrounding medium to
make water (H2O). The removal of the hydrogen ions from the system
contributes to the ion gradient used in the process of chemiosmosis.
Chemiosmosis
In chemiosmosis, the free energy from the series of redox reactions just
described is used to pump hydrogen ions (protons) across the membrane
(from inside the matrix into the intermembrane space). The uneven
distribution of H* ions across the membrane establishes both concentration
and electrical gradients (thus, an electrochemical gradient), sue to the
hydrogen ions’ positive charge and their aggregation on one side of the
membrane. This electrochemical gradient is a form of potential energy, and
its discovery was a key step in Mitchell's elucidation of the details of
oxidative phosphorylation.
If the membrane was not a barrier to the movement of the hydrogen ions,
the ions would diffuse back across into the matrix, driven by their
electrochemical gradient. But recall that many ions cannot diffuse through
the nonpolar regions of phospholipid membranes without the aid of ion
channels. Similarly, hydrogen ions in the intermembrane space can only
pass through the inner mitochondrial membrane through an integral
membrane protein called ATP synthase ([link]). This complex protein acts
as a tiny generator, turned by the force of the hydrogen ions diffusing down
their electrochemical gradient via a channel in the protein. This powers an
actual rotation of parts of the enzyme; the rotation of parts of this molecular
machine facilitates the addition of a phosphate to ADP, forming ATP. In the
absence of a hydrogen ion gradient, the rotation stops and no ATP is made.
ATP Synthase
Intermembrane Inner mitochondrial
space membrane
Vatarpvarprarecarppipay: Wp p'p'p'P aah ata hatang?
UAL eR
Mitochondrial
matrix
ATP synthase is a complex,
molecular machine that uses a
proton (H*) gradient to form ATP
from ADP and inorganic
phosphate (Pi). (Credit:
modification of work by Klaus
Hoffmeier)
Chemiosmosis ([link]) is used to generate 90 percent of the ATP made
during aerobic cellular respiration; it is also the method used in the light
reactions of photosynthesis to harness the energy of sunlight in the process
of photophosphorylation. Recall that the production of ATP using the
process of chemiosmosis in mitochondria is called oxidative
phosphorylation. The overall result of these reactions is the production of
about 32 ATP from the energy of the electrons removed from hydrogen
atoms ([link]). These electrons were originally part of a glucose molecule.
At the end of the pathway, the electrons are used to reduce an oxygen
molecule to oxygen ions. The extra electrons on the oxygen attract
hydrogen ions (protons) from the surrounding medium, and water is
formed.
Intermembrane space
+ + +
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In oxidative phosphorylation, the hydrogen
ion electrochemical gradient, generated by
the electron transport chain, is used by ATP
synthase to form ATP.
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Oxidative Phosphorylation
This image is an overview of oxidative phosphorylation. During this
stage, the electrons from NADH and FADH? are used to produce a
large amount of ATP (~32). (Image by Eva Horne and Robert Bear)
ATP Yield
The number of ATP molecules generated from the catabolism of glucose
can be variable. For example, the number of hydrogen ions that the electron
transport chain complexes can pump through the membrane varies between
species. Another source of variance stems from the shuttle of electrons
across the membranes of the mitochondria. (The NADH generated from
glycolysis cannot easily enter mitochondria.) Thus, electrons are picked up
on the inside of mitochondria by either NAD* or FAD*. As you have
learned earlier, these FAD* molecules carry electrons that are lower in
energy than those on NADH; consequently, fewer ATP molecules are
generated when FAD” acts as a carrier. NAD* is used as the electron
transporter in the liver and FAD” acts in the brain. Assuming optimal ATP
production, a net of 2 are formed in glycolysis, 2 are formed in the Kreb's
cycle, and 32 produced during oxidative phophorylation ({link]). The total
amount of ATP formed form 1 molecule of glucose is generally around 36
under optimal conditions.
Cytoplasm
H,O O,
Y
Oxidative
Phosphory-
lation
Aerobic Cellular Respiration
This image is an overview of aerobic cellular respiration showing the
number of ATP produced by the various steps of the process.
Assuming optimal conditions, there are 36 ATP molecules produced
for each molecule of glucose entering aerobic cellular respiration.
(Image by Eva Horne and Robert Bear)
Another factor that affects the yield of ATP molecules generated from
glucose is the fact that intermediate compounds and electron carriers in
these pathways are used for other purposes. Glucose catabolism connects
with the pathways that build or break down all other biochemical
compounds in cells, and the result is that some metabolites (e.g. pyruvate)
are shuttled off for other purposes. Additionally, sugars other than glucose
are fed into various steps in the glycolytic pathway for energy extraction.
The five-carbon sugars that form nucleic acids are made from intermediates
in glycolysis. Certain nonessential amino acids can be made from
intermediates of both glycolysis and the Krebs cycle. Lipids, such as
cholesterol and triglycerides, are also made from acetyl-CoA, and both
amino acids and triglycerides are broken down for energy, feeding into
these pathways at various places. NADH is used by other redox reactions in
cells, which means that not all of the high energy electrons liberated from
glucose are used in oxidative phosphorylation. So the tidy pictures above
don't really reflect the complexity of metabolism in a living cell. So the
relationship between glucose breakdown and ATP production is like all
relationships: "It's complicated."
Codependency of Photosynthesis and Aerobic Cellular
Respiration
As you may have noticed, the substrates of aerobic cellular respiration are
the products of photosynthesis, and the substrates of photosynthesis are the
products of aerobic cellular respiration ([link]). These two processes are
interdependent; they have been evolving with one another for a very long
time and are important components of the carbon cycle and obviously the
flow of energy. In this section, we will take a closer look at the
codependency of photosynthesis and cellular respiration.
H,O O, Cytoplasm
Oxidative
Phosphory-
Aerobic Cellular Respiration
This image shows the interrelatedness of photosynthesis and aerobic
cellular respiration Note how the the two processes are almost mirror
images of each other. (Image by Eva Horne and Robert Bear)
The first point of interaction is the cycling of water and oxygen. During
photosynthesis, oxygen gas is produced and the source of the oxygen atoms
is the reactant water. The oxygen is formed in the initial step of
photosynthesis, when photosystem II splits a water molecule into oxygen
gas, hydrogen ions and electrons. In the light dependent reactions on the
thylakoid membrane, light energy is absorbed and transferred to ATP and
NADP. The light energy is transferred to chemical energy during this
process. In aerobic cellular respiration, the roles are reversed: oxygen is the
reactant, and water is the product. The aerobic cellular respiration process
uses oxygen in the final (not initial) step, when it merges (rather than
splitting) with the electrons and hydrogen ions during oxidative
phosphorylation. The cycling of water and oxygen between photosynthesis
and aerobic cellular respiration is the source of electrons that harvest, store
and transfer energy.
Another product of photosynthesis is Glucose (carbohydrate). In the Calvin
cycle, carbohydrates are produced by fixing carbon dioxide (reactant) and
by adding energy from ATP and NADPH. During aerobic cellular
respiration, NADH and FADH) capture the energy stored in glucose
(reactant). The captured energy in NADH and FADH)j is then used during
oxidative phospholrylation to produce ATP. This process of energy capture
also releases a waste product - carbon dioxide. So energy from the sun is
used to make glucose from COs, which is a nutrient for the plant. The
product of photosynthesis (glucose) contains that nutrient AND the energy
derived from sunlight; glcuose is thus a high energy nutrient for
heterotrophic organisms. These organisms release the nutrient as CO» and
use some of the energy to do cellular work. Other energy is lost as heat. It
should be obvious that nutrients cycle between autotrophs and heterotrophs,
while energy moves in a one-way direction from autotrophs to heterotrophs.
Photosynthesis and aerobic cellular respiration are codependent; they rely
upon use each other’s products and byproducts and are essentially the
opposites of each other. Neither process can happen without the other
because if there is no carbon dioxide, photosynthesis cannot proceed; and if
there is no oxygen, aerobic cellular respiration cannot proceed. The
exergonic reactions of cellular respiration (glycolysis, Kreb’s cycle and
oxidative phosphorylation) mirror the energonic reactions of photosynthesis
(Light Dependent Reactions and Calvin cycle). As we learned on the
ecosystem level, nutrients cycle and energy flows. The same is true on the
cellular level: nutrients cycle and energy flows.
Metabolism Without Oxygen
"Not all chemicals are bad. Without chemicals such as hydrogen and
oxygen, for example, there would be no way to make water, a vital
ingredient in beer." - Dave Barry
The other vital ingredient in beer, of course, is ethanol. And ethanol is one
of the more important products of anaerobic respiration. Other compounds,
such as lactic acid, are also metabolic by-products of respiration in the
absence of oxygen. The key purpose of all of these metabolic pathways is
the need to regenerate NAD from the NADH produced during glycolysis. In
aerobic respiration, NADH donates those electrons to the electron transfer
chain. Recall that the final electron acceptor in that pathway is an oxygen
molecule, O>. If oxygen is present, then ATP will be produced using the
energy of high-energy electrons carried by NADH or FADH> to the electron
transport chain. If oxygen is not present, NADH must be reoxidized to
NAD‘ for reuse as an electron carrier for the glycolytic pathway to
continue. How is this done? Some living systems use an organic molecule
as the final electron acceptor. Processes that use an organic molecule to
regenerate NAD* from NADH are collectively referred to as fermentation
(anaerobic metabolism). In contrast, some living systems use an inorganic
molecule as a final electron acceptor of the electron transport chain, and this
process is called anaerobic cellular respiration in which organisms
convert energy for their use in the absence of oxygen.
Anaerobic Metabolism
Certain prokaryotes, including some species of bacteria and Archaea, use
anaerobic respiration. For example, the group of Archaea called
methanogens reduces carbon dioxide to methane to oxidize NADH. These
microorganisms are found in soil and in the digestive tracts of ruminants,
such as cows and sheep. Similarly, sulfate-reducing bacteria and Archaea,
most of which are anaerobic ( [link]), reduce sulfate to hydrogen sulfide to
regenerate NAD* from NADH.
The green color seen in these coastal waters
is from an eruption of hydrogen sulfide-
producing bacteria. These anaerobic, sulfate-
reducing bacteria release hydrogen sulfide
gas as they decompose algae in the water.
(credit: modification of work by NASA/Jeff
Schmaltz, MODIS Land Rapid Response
Team at NASA GSFC, Visible Earth
Catalog of NASA images)
Lactic Acid Fermentation
The fermentation method used by animals and certain bacteria, like those in
yogurt, is lactic acid fermentation ( [link]). This type of fermentation is
used routinely in mammalian red blood cells and in skeletal muscle that has
an insufficient oxygen supply to allow aerobic respiration to continue (that
is, in muscles used to the point of fatigue). In muscles, lactic acid
accumulation must be removed by the blood circulation and the lactate
brought to the liver for further metabolism.
Cytoplasm
Lactic acid fermentation is common in muscle cells that
have run out of oxygen. (Image by Robert Bear)
Alcohol Fermentation
Another familiar fermentation process is alcohol fermentation ( [link]) that
produces ethanol, an alcohol. The first chemical reaction of alcohol
fermentation is the following (CO> does not participate in the second
reaction):
The first reaction is catalyzed by pyruvate decarboxylase, a cytoplasmic
enzyme, with a coenzyme of thiamine pyrophosphate (TPP, derived from
vitamin B, and also called thiamine). A carboxyl group is removed from
pyruvate, releasing carbon dioxide as a gas. The loss of carbon dioxide
reduces the size of the molecule by one carbon, making acetaldehyde. The
second reaction is catalyzed by alcohol dehydrogenase to oxidize NADH to
NAD* and reduce acetaldehyde to ethanol. The fermentation of pyruvate by
yeast produces the ethanol found in alcoholic beverages. Ethanol tolerance
of yeast is variable, ranging from about 5 percent to 21 percent, depending
on the yeast strain and environmental conditions.
YAP
Alcohol fermentation is occurs in fungi and plants with
carbon dioxide and alcohol as the byproducts. (Image by
Robert Bear)
= Cytoplasm a -
Other Types of Fermentation
Other fermentation methods occur in bacteria. Many prokaryotes are
facultatively anaerobic. This means that they can switch between aerobic
respiration and fermentation, depending on the availability of oxygen.
Certain prokaryotes, like Clostridia, are obligate anaerobes. Obligate
anaerobes live and grow in the absence of molecular oxygen. Oxygen is a
poison to these microorganisms and kills them on exposure. It should be
noted that all forms of fermentation, except lactic acid fermentation,
produce gas. The production of particular types of gas is used as an
indicator of the fermentation of specific carbohydrates, which plays a role
in the laboratory identification of the bacteria. Various methods of
fermentation are used by assorted organisms to ensure an adequate supply
of NAD* for the sixth step in glycolysis. Without these pathways, that step
would not occur and no ATP would be harvested from the breakdown of
glucose.
Connections of Carbohydrate, Protein, and Lipid Metabolic Pathways
Introduction
" SIR TOBY: Does not our lives consist of the four elements? / SIR
ANDREW: Faith, so they say; but I think it rather consists of eating and
drinking. / SIR TOBY: Thou'rt a scholar; let us therefore eat and drink. "
William Shakespeare, Twelfth Night
You have learned about the catabolism of glucose, which provides energy to
living cells. But when you eat and drink, as advised by Sir Toby, you
consume more than glucose for food. How does a turkey/avocado sandwich
end up as ATP in your cells? This happens because all of the catabolic
pathways for carbohydrates, proteins, and lipids eventually connect into
glycolysis and the Krebs cycle pathways (see [link]). Metabolic pathways
should be thought of as porous—that is, substances enter from other
pathways, and intermediates leave for other pathways. These pathways are
not closed systems. Many of the substrates, intermediates, and products in a
particular pathway are reactants in other pathways.
Connections of Other Sugars to Glucose Metabolism
Glycogen, a polymer of glucose, is an energy storage molecule in animals.
When there is adequate ATP present, excess glucose is shunted into
glycogen for storage. Glycogen is made and stored in both liver and muscle.
The glycogen will be hydrolyzed into glucose monomers (G-1-P) if blood
sugar levels drop. The presence of glycogen as a source of glucose allows
ATP to be produced for a longer period of time during exercise. Glycogen is
broken down into G-1-P and converted into G-6-P in both muscle and liver
cells, and this product enters the glycolytic pathway.
Sucrose is a disaccharide with a molecule of glucose and a molecule of
fructose bonded together with a glycosidic linkage. Fructose is one of the
three dietary monosaccharides, along with glucose and galactose (which is
part of the milk sugar, the disaccharide lactose), which are absorbed directly
into the bloodstream during digestion. The catabolism of both fructose and
galactose produces the same number of ATP molecules as glucose.
Connections of Proteins to Glucose Metabolism
Proteins are hydrolyzed by a variety of enzymes in cells. Most of the time,
the amino acids are recycled into the synthesis of new proteins. If there are
excess amino acids, however, or if the body is in a state of starvation, some
amino acids will be shunted into the pathways of glucose catabolism
({link]). Each amino acid must have its amino group removed prior to entry
into these pathways. The amino group is converted into ammonia. In
mammals, the liver synthesizes urea from two ammonia molecules and a
carbon dioxide molecule. Thus, urea is the principal waste product in
mammals produced from the nitrogen originating in amino acids, and it
leaves the body in urine.
Phosphoenolpyruvate Alanine Glycine Threonine
Cysteine Serine Tryptophan
fl ovate
ine
Glucose Acetyl CoA [> = Acetoacetate
Leucine
Lysine
Phenylalanine
Oxaloacetate Citrate Tyrosine
Tryptophan
Asparagine / \
Aspartate Anis Peal
: rginine Proline
Malate onal Histidine Glutamine
Fumarate a-Ketoglutarate Glutamate
Tyrosine \ F F / Isoleucine Valine
Phenylalanine a ee a CoA Methionine Threonine
The carbon skeletons of certain amino acids (indicated in
boxes) derived from proteins can feed into the Krebs
cycle. (credit: modification of work by Mikael
Haggstrém)
Connections of Lipid and Glucose Metabolisms
The lipids that are connected to the glucose pathways are cholesterol and
triglycerides. Cholesterol is a lipid that contributes to plasma membrane
flexibility and is a precursor of steroid hormones. The synthesis of
cholesterol starts with acetyl groups and proceeds in only one direction. The
process cannot be reversed.
Triglycerides are a form of long-term energy storage in animals.
Triglycerides are made of glycerol and three fatty acids. Animals can make
most of the fatty acids they need. Triglycerides can be both made and
broken down through parts of the glucose catabolism pathways. Glycerol
can be phosphorylated to glycerol-3-phosphate, which continues through
glycolysis. Fatty acids are catabolized in a process called beta-oxidation
that takes place in the matrix of the mitochondria and converts their fatty
acid chains into two carbon units of acetyl groups. The acetyl groups are
picked up by CoA to form acetyl-CoA that proceeds into the Krebs cycle.
<€ ———
Acetyl-CoA
~
BET Amino Acids
Glycogen from the liver and muscles, hydrolyzed
into glucose-1-phosphate, together with fats and
proteins, can feed into the catabolic pathways for
carbohydrates. Work by Eva Horne and Robert A.
Bear.
Note:
Evolution Connection
Pathways of Photosynthesis and Cellular Metabolism
The processes of photosynthesis and cellular metabolism consist of several
very complex pathways. It is generally thought that the first cells arose in
an aqueous environment—a “soup” of nutrients—probably on the surface
of some porous clays. If these cells reproduced successfully and their
numbers climbed steadily, it follows that the cells would begin to deplete
the nutrients from the medium in which they lived as they shifted the
nutrients into the components of their own bodies. This hypothetical
situation would have resulted in natural selection favoring those organisms
that could exist by using the nutrients that remained in their environment
and by manipulating these nutrients into materials upon which they could
survive. Selection would favor those organisms that could extract maximal
value from the nutrients to which they had access.
An early form of photosynthesis developed that harnessed the sun’s energy
did not use water as a source of hydrogen atoms, and did not produce free
oxygen (anoxygenic photosynthesis). Early photosynthesis did not produce
free oxygen because it did not use water as the source of hydrogen ions;
instead, it used materials like hydrogen sulfide and consequently produced
sulfur. It is thought that glycolysis developed at this time and could take
advantage of the simple sugars being produced, but these reactions were
unable to fully extract the energy stored in the carbohydrates. The
development of glycolysis probably predated the evolution of
photosynthesis, as it was well suited to extract energy from materials
spontaneously accumulating in the “primeval soup.” A later form of
photosynthesis used water as a source of electrons and hydrogen, and
generated free oxygen. Over time, the atmosphere became oxygenated, but
not before the oxygen released oxidized metals in the ocean and created a
“rust” layer in the sediment, permitting the dating of the rise of the first
oxygenic photosynthesizers. Living things adapted to exploit this new
atmosphere that allowed aerobic respiration as we know it to evolve. When
the full process of oxygenic photosynthesis developed and the atmosphere
became oxygenated, cells were finally able to use the oxygen expelled by
photosynthesis to extract considerably more energy from the sugar
molecules using the Krebs cycle and oxidative phosphorylation.
Prokaryote Structure
By the end of this section, you will be able to do the following:
e Describe the basic structure of a typical prokaryote
e Describe important differences in structure between Archaea and
Bacteria
"For the first half of geological time our ancestors were bacteria. Most
creatures still are bacteria, and each one of our trillions of cells is a colony
of bacteria." Richard Dawkins
There are many differences between prokaryotic and eukaryotic cells. The
name "prokaryote" suggests that prokaryotes are defined by exclusion—
they are not eukaryotes, or organisms whose cells contain a nucleus and
other internal membrane-bound organelles. However, all cells have four
common structures: the plasma membrane, which functions as a barrier for
the cell and separates the cell from its environment; the cytoplasm, a
complex solution of organic molecules and salts inside the cell; a double-
stranded DNA genome, the informational archive of the cell; and
ribosomes, where protein synthesis takes place. Prokaryotes come in
various shapes, but many fall into three categories: cocci (spherical), bacilli
(rod-shaped), and spirilli (spiral-shaped) ({link]).
(a) (b) (c)
Common prokaryotic cell types. Prokaryotes fall into three
basic categories based on their shape, visualized here using
scanning electron microscopy: (a) cocci, or spherical (a pair is
shown); (b) bacilli, or rod-shaped; and (c) spirilli, or spiral-
shaped. (credit a: modification of work by Janice Haney Carr,
Dr. Richard Facklam, CDC; credit c: modification of work by
Dr. David Cox; scale-bar data from Matt Russell)
The Prokaryotic Cell
Recall that prokaryotes are unicellular organisms that lack membrane-
bound organelles or other internal membrane-bound structures ({link]).
Their chromosome—usually single—consists of a piece of circular, double-
stranded DNA located in an area of the cell called the nucleoid. Most
prokaryotes have a cell wall outside the plasma membrane. The cell wall
functions as a protective layer, and it is responsible for the organism’s
shape. Some bacterial species have a capsule outside the cell wall. The
capsule enables the organism to attach to surfaces, protects it from
dehydration and attack by phagocytic cells, and makes pathogens more
resistant to our immune responses. Some species also have flagella
(singular, flagellum) used for locomotion, and pili (singular, pilus) used for
attachment to surfaces including the surfaces of other cells. Plasmids, which
consist of extra-chromosomal DNA, are also present in many species of
bacteria and archaea.
Cell
membrane
Ribosome
Chromosome Nucleoid region
(DNA)
The features of a typical
prokaryotic cell. Flagella,
capsules, and pili are not found in
all prokaryotes.
Recall that prokaryotes are divided into two different domains, Bacteria and
Archaea, which together with Eukarya, comprise the three domains of life
(Link]).
Euryarchaeotes
Crenachaeotes
Nanoarchaeotes
Korarchaeotes
Proteobacteria
Chlamydias
Spirochetes
Cyanobacteria
Gram-Positive bacteria
The three domains of living organisms. Bacteria
and Archaea are both prokaryotes but differ
enough to be placed in separate domains. An
ancestor of modern Archaea is believed to have
given rise to Eukarya, the third domain of life.
Major groups of Archaea and Bacteria are
shown.
Characteristics of bacterial phyla are described in [link] and [link]. Major
bacterial phyla include the Proteobacteria, the Chlamydias, the
Spirochaetes, the photosynthetic Cyanobacteria, and the Gram-positive
bacteria. The Proteobacteria are in turn subdivided into several classes,
from the Alpha- to the Epsilon proteobacteria. Eukaryotic mitochondria are
thought to be the descendants of alphaproteobacteria, while eukaryotic
chloroplasts are derived from cyanobacteria. Archaeal phyla are described
in [Link].
Bacteria of Phylum Proteobacteria
Alpha Proteobacteria Rhizobium
Some species are photoautotrophic Nitrogen-fixing endosymbiont
but some are symbionts of plants associated with the roots of legumes
and animals and others are
pathogens. Eukaryotic mitochondria Rickettsia
are thought be derived from bacteria Obligate intracellular parasite that
in this group. causes typhus and Rocky Mountain
Spotted Fever (but not rickets,
which is caused by Vitamin C Rickettsia rickettsia, stained red, grow
deficiency) inside a host cell.
Beta Proteobacteria Nitrosomas
This group of bacteria is diverse. Species from this group oxidize
Some species play an important ammonia into nitrite.
role in the nitrogen cycle.
Spirillum minus
Causes rat-bite fever
Gamma Proteobacteria Escherichia coli
Many are beneficial symbionts that Normally beneficial microbe of
populate the human gut, but others the human gut, but some strains
are familiar human pathogens. cause disease
Some species from this subgroup
oxidize sulfur compounds. Salmonella
Certain strains cause food
poisoning or typhoid fever
Vibrio cholera
Yersinia pestis
Causative agent of Bubonic plague
Psuedomonas aeruginosa
Causes lung infections
Vibrio cholera
Causative agent of cholera
Chromatium
Sulfur-producing bacteria that
oxidize sulfur, producing H»S
Delta Proteobacteria Myxobacteria
Some species generate a Generate spore-forming fruiting
spore-forming fruiting body in bodies in adverse conditions
adverse conditions. Others
reduce sulfate and sulfur. Desulfovibrio vulgaris
Aneorobic, sulfate-reducing L* Le
| —
bacterium > ~ 500 nm"
Desulfovibrio vulgaris
Epsilon Proteobacteria Campylobacter
Many species inhabit the digestive Causes blood poisoning and
tract of animals as symbionts or intestinal inflammation
pathogens. Bacteria from this group f -
have been found in deep-sea Heliobacter pylori
hydrothermal vents and cold seep Causes stomach ulcers
habitats. 9 e 500 hm
Campylobacter
The Proteobacteria. Phylum Proteobacteria is one of up to 52
bacteria phyla. Proteobacteria is further subdivided into five
classes, Alpha through Epsilon. (credit “Rickettsia rickettsia”:
modification of work by CDC; credit “Spirillum minus”:
modification of work by Wolframm Adlassnig; credit “Vibrio
cholera”: modification of work by Janice Haney Carr, CDC;
credit “Desulfovibrio vulgaris”: modification of work by
Graham Bradley; credit “Campylobacter”: modification of
work by De Wood, Pooley, USDA, ARS, EMU; scale-bar data
from Matt Russell)
Bacteria: Chlamydia, Spirochaetae, Cyanobacteria, and Gram-positive
Chlamydias
All members of this group are
obligate intracellular parasites of animal
cells. Cells walls lack peptidoglycan.
Spirochetes
Most members of this species,
which has spiral-shaped cells, are
free-living aneaerobes, but some are
pathogenic. Flagella run lengthwise in the
periplasmic space between the inner and
outer membrane.
Cyanobacteria
Also known as blue-green algae,
these bacteria obtain their energy through
photosynthesis. They are ubiquitous,
found in terrestrial, marine, and freshwater
environments. Eukaryotic chloroplasts are
thought be derived from bacteria in this
group.
Gram-positive Bacteria
Soil-dwelling members of this subgroup
decompose organic matter. Some species
cause disease. They have a thick cell wall
and lack an outer membrane.
Chlamydia trachomatis
Common sexually transmitted
disease that can lead to blindness
Treponema pallidum
Causative agent of syphilis
Borrelia burgdorferi
Causative agent of Lyme disease
Prochlorococcus
Believed to be the most abundant
photosynthetic organism on earth;
responsible for generating half
the world’s oxygen
Bacillus anthracis
Causes anthrax
Clostridium botulinum
Causes Botulism
Clostridium difficile
Causes diarrhea during antibiotic
therapy
Streptomyces
Many antibiotics, including
streptomyocin, are derived from
these bacteria.
Mycoplasmas
These tiny bacteria, the smallest
known, lack a cell wall.
Some are free-living, and some
are pathogenic.
—<s
b — \
CZ #10 yum
In this pap smear, Chlamydia trachomatis
appear as pink inclusions inside cells.
Treponema pallidum
2 Om
Phormidium
A.
, “© °70 pn
Clostridium difficile
Other bacterial phyla. Chlamydia, Spirochetes, Cyanobacteria,
and Gram-positive bacteria are described in this table. Note
that bacterial shape is not phylum-dependent; bacteria within a
phylum may be cocci, rod-shaped, or spiral. (credit
“Chlamydia trachomatis”: modification of work by Dr. Lance
Liotta Laboratory, NCI; credit “Treponema pallidum”:
modification of work by Dr. David Cox, CDC; credit
“Phormidium”: modification of work by USGS; credit
“Clostridium difficile”: modification of work by Lois S.
Wiggs, CDC; scale-bar data from Matt Russell)
Euryarchaeota
This phylum includes
methanogens, which produce
methane as a metabolic waste
product, and halobacteria,
which live in an extreme saline
environment.
Crenarchaeota
Members of the ubiquitous
phylum play an important role
in the fixation of carbon. Many
members of this group are
sulfur-dependent extremophiles.
Some are thermophilic or
hyperthermophilic.
Nanoarchaeota
This group currently contains
only one species,
Nanoarchaeum equitans.
Korarchaeota
Members of this phylum,
considered to be one of the
most primitive forms of life,
have only been found in the
Obsidian Pool, a hot spring at
Yellowstone National Park.
Methanogens
Methane production causes
flatulence in humans and other
animals.
Halobacteria
Large blooms of this salt-loving
archaea appear reddish due to
the presence of bacterirhodopsin
in the membrane.
Bacteriorhodopsin is related to
the retinal pigment rhodopsin.
Sulfolobus
Members of this genus grow
in volcanic springs at
temperatures between 75° and
80°C and at a pH between
2 and 3.
ium
Sulfolobus being infected by bacteriophage
Nanoarchaeum equitans
This species was isolated from
the bottom of the Atlantic Ocean
and from a hydrothermal vent
at Yellowstone National Park.
It is an obligate symbiont with
Ignicoccus, another species of
archaea.
Nanoarchaeum equitans (small dark spheres) are
in contact with their larger host, /gnicoccus.
No members of this species
have been cultivated.
y
wv a .
This image shows a variety of korarchaeota species
from the Obsidian Pool at Yellowstone National Park.
Archaeal phyla. Archaea are separated into four phyla: the
Korarchaeota, Euryarchaeota, Crenarchaeota, and
Nanoarchaeota. (credit “Halobacterium”: modification of
work by NASA; credit “Nanoarchaeotum equitans”:
modification of work by Karl O. Stetter; credit “Korarchaeota”
modification of work by Office of Science of the U.S. Dept. of
Energy; scale-bar data from Matt Russell)
The Plasma Membrane of Prokaryotes
The prokaryotic plasma membrane is a thin lipid bilayer (6 to 8
nanometers) that completely surrounds the cell and separates the inside
from the outside. Its selectively permeable nature keeps ions, proteins, and
other molecules within the cell and prevents them from diffusing into the
extracellular environment, while other molecules may move through the
membrane. Recall that the general structure of a cell membrane is a
phospholipid bilayer composed of two layers of lipid molecules. In archaeal
cell membranes, isoprene (phytanyl) chains linked to glycerol replace the
fatty acids linked to glycerol in bacterial membranes. Some archaeal
membranes are lipid monolayers instead of bilayers ({link]).
Phospholipid from ® Phytanyl
Archaea 7 sidechain
@® Ether linkage
Phospholipid from Bacteria Ester linkage
and Eukarya
Glycerol
Phosphate group
OS SE OO
OES SED Oa
OS SD ORE
Phospholipid bilayer from Phospholipid bilayer from
Bacteria and Eukarya Archaea
Bacterial and archaeal
phospholipids. Archaeal
phospholipids differ from those
found in Bacteria and Eukarya in
two ways. First, they have
branched phytanyl sidechains
instead of linear ones. Second, an
ether bond instead of an ester bond
connects the lipid to the glycerol.
The Cell Wall of Prokaryotes
The cytoplasm of prokaryotic cells has a high concentration of dissolved
solutes. Therefore, the osmotic pressure within the cell is relatively high.
The cell wall is a protective layer that surrounds some cells and gives them
shape and rigidity. It is located outside the cell membrane and prevents
osmotic lysis (bursting due to increasing volume). The chemical
composition of the cell wall varies between Archaea and Bacteria, and also
varies between bacterial species.
Bacterial cell walls contain peptidoglycan, composed of polysaccharide
chains that are cross-linked by unusual peptides containing both L- and D-
amino acids including D-glutamic acid and D-alanine. (Proteins normally
have only L-amino acids; as a consequence, many of our antibiotics work
by mimicking D-amino acids and therefore have specific effects on
bacterial cell-wall development.) There are more than 100 different forms
of peptidoglycan. S-layer (surface layer) proteins are also present on the
outside of cell walls of both Archaea and Bacteria.
Bacteria are divided into two major groups: Gram positive and Gram
negative, based on their reaction to Gram staining. Note that all Gram-
positive bacteria belong to one phylum; bacteria in the other phyla
(Proteobacteria, Chlamydias, Spirochetes, Cyanobacteria, and others) are
Gram-negative. The Gram staining method is named after its inventor,
Danish scientist Hans Christian Gram (1853-1938). The different bacterial
responses to the staining procedure are ultimately due to cell wall structure.
Gram-positive organisms typically lack the outer membrane found in
Gram-negative organisms ({link]). Up to 90 percent of the cell-wall in
Gram-positive bacteria is composed of peptidoglycan, and most of the rest
is composed of acidic substances called teichoic acids. Teichoic acids may
be covalently linked to lipids in the plasma membrane to form lipoteichoic
acids. Lipoteichoic acids anchor the cell wall to the cell membrane. Gram-
negative bacteria have a relatively thin cell wall composed of a few layers
of peptidoglycan (only 10 percent of the total cell wall), surrounded by an
outer envelope containing lipopolysaccharides (LPS) and lipoproteins. This
outer envelope is sometimes referred to as a second lipid bilayer. The
chemistry of this outer envelope is very different, however, from that of the
typical lipid bilayer that forms plasma membranes.
Note:
Visual Connection
poteichoic acid —_ Lipopolysaccharide Porin
Lipoprotein
Outer
Peptidoglycan #\ membrane
cell wal Periplasmic
space
L ene Inner
L sane membrane
Gram-positive bacteria Gram-negative bacteria
Cell walls in Gram-positive and Gram-negative bacteria.
Bacteria are divided into two major groups: Gram positive and
Gram negative. Both groups have a cell wall composed of
peptidoglycan: in Gram-positive bacteria, the wall is thick,
whereas in Gram-negative bacteria, the wall is thin. In Gram-
negative bacteria, the cell wall is surrounded by an outer
membrane that contains lipopolysaccharides and lipoproteins.
Porins are proteins in this cell membrane that allow substances
to pass through the outer membrane of Gram-negative bacteria.
In Gram-positive bacteria, lipoteichoic acid anchors the cell
wall to the cell membrane. (credit: modification of work by
"Franciscosp2"/Wikimedia Commons)
Which of the following statements is true?
a. Gram-positive bacteria have a single cell wall anchored to the cell
membrane by lipoteichoic acid.
b. Porins allow entry of substances into both Gram-positive and Gram-
negative bacteria.
c. The cell wall of Gram-negative bacteria is thick, and the cell wall of
Gram-positive bacteria is thin.
d. Gram-negative bacteria have a cell wall made of peptidoglycan,
whereas Gram-positive bacteria have a cell wall made of lipoteichoic
acid.
Archaean cell walls do not have peptidoglycan. There are four different
types of archaean cell walls. One type is composed of
pseudopeptidoglycan, which is similar to peptidoglycan in morphology but
contains different sugars in the polysaccharide chain. The other three types
of cell walls are composed of polysaccharides, glycoproteins, or pure
protein. Other differences between Bacteria and Archaea are seen in [link].
Note that features related to DNA replication, transcription and translation
in Archaea are similar to those seen in eukaryotes.
Differences and Similarities between Bacteria and Archaea
Baffestencds and Similarities between Bacteria and Archaea
Characteristic
Structural
Characteristic
Cell type
Cell morphology
Cell wall
Cell membrane
type
Plasma membrane
lipids
Chromosome
Replication
origins
RNA polymerase
Initiator tRNA
Streptomycin
inhibition
Calvin cycle
Bacteria
Bacteria
Prokaryotic
Variable
Contains
peptidoglycan
Lipid bilayer
Fatty acids-
glycerol ester
Typically circular
Single
Single
Formyl-
methionine
Sensitive
Yes
Archaea
Archaea
Prokaryotic
Variable
Does not contain
peptidoglycan
Lipid bilayer or lipid
monolayer
Phytanyl-glycerol
ethers
Typically circular
Multiple
Multiple
Methionine
Resistant
No
Reproduction
Reproduction in prokaryotes is asexual and usually takes place by binary
fission. (Recall that the DNA of a prokaryote is a single, circular
chromosome.) Prokaryotes do not undergo mitosis; instead, the
chromosome is replicated and the two resulting copies separate from one
another, due to the growth of the cell. The prokaryote, now enlarged, is
pinched inward at its equator and the two resulting cells, which are clones,
separate. Binary fission does not provide an opportunity for genetic
recombination or genetic diversity, but prokaryotes can share genes by three
other mechanisms.
In transformation, the prokaryote takes in DNA shed by other prokaryotes
into its environment. If a nonpathogenic bacterium takes up DNA for a
toxin gene from a pathogen and incorporates the new DNA into its own
chromosome, it too may become pathogenic. In transduction,
bacteriophages, the viruses that infect bacteria, may move short pieces of
chromosomal DNA from one bacterium to another. Transduction results in
a recombinant organism. Archaea also have viruses that may translocate
genetic material from one individual to another. In conjugation, DNA is
transferred from one prokaryote to another by means of a pilus, which
brings the organisms into contact with one another, and provides a channel
for transfer of DNA. The DNA transferred can be in the form of a plasmid
or as a composite molecule, containing both plasmid and chromosomal
DNA. These three processes of DNA exchange are shown in [link].
Reproduction can be very rapid: a few minutes for some species. This short
generation time coupled with mechanisms of genetic recombination and
high rates of mutation result in the rapid evolution of prokaryotes, allowing
them to respond to environmental changes (such as the introduction of an
antibiotic) very quickly.
Pop
BB
(a) Transformation (b) Transduction (c) Conjugation
Gene transfer mechanisms in prokaryotes. There are three mechanisms
by which prokaryotes can exchange DNA. In (a) transformation, the
cell takes up prokaryotic DNA directly from the environment. The
DNA may remain separate as plasmid DNA or be incorporated into the
host genome. In (b) transduction, a bacteriophage injects DNA into the
cell that contains a small fragment of DNA from a different
prokaryote. In (c) conjugation, DNA is transferred from one cell to
another via a mating bridge, or pilus, that connects the two cells after
the sex pilus draws the two bacteria close enough to form the bridge.
Note:
Evolution Connection
The Evolution of Prokaryotes
How do scientists answer questions about the evolution of prokaryotes?
Unlike with animals, artifacts in the fossil record of prokaryotes offer very
little information. Fossils of ancient prokaryotes look like tiny bubbles in
rock. Some scientists turn to genetics and to the principle of the molecular
clock, which holds that the more recently two species have diverged, the
more similar their genes (and thus proteins) will be. Conversely, species
that diverged long ago will have more genes that are dissimilar.
Scientists at the NASA Astrobiology Institute and at the European
Molecular Biology Laboratory collaborated to analyze the molecular
evolution of 32 specific proteins common to 72 species of prokaryotes.
[footnote] The model they derived from their data indicates that three
important groups of bacteria—Actinobacteria, Deinococcus, and
Cyanobacteria (collectively called Terrabacteria by the authors)—were the
first to colonize land. Actinobacteria are a group of very common Gram-
positive bacteria that produce branched structures like fungal mycelia, and
include species important in decomposition of organic wastes. You will
recall that Deinococcus is a genus of bacterium that is highly resistant to
ionizing radiation. It has a thick peptidoglycan layer in addition to a second
external membrane, so it has features of both Gram-positive and Gram-
negative bacteria.
Battistuzzi, FU, Feijao, A, and Hedges, SB. A genomic timescale of
prokaryote evolution: Insights into the origin of methanogenesis,
phototrophy, and the colonization of land. BioMed Central: Evolutionary
Biology 4 (2004): 44, doi:10.1186/1471-2148-4-44.
Cyanobacteria are photosynthesizers, and were probably responsible for
the production of oxygen on the ancient earth. The timelines of divergence
suggest that bacteria (members of the domain Bacteria) diverged from
common ancestral species between 2.5 and 3.2 billion years ago, whereas
the Archaea diverged earlier: between 3.1 and 4.1 billion years ago.
Eukarya later diverged from the archaean line. The work further suggests
that stromatolites that formed prior to the advent of cyanobacteria (about
2.6 billion years ago) photosynthesized in an anoxic environment and that
because of the modifications of the Terrabacteria for land (resistance to
drying and the possession of compounds that protect the organism from
excess light), photosynthesis using oxygen may be closely linked to
adaptations to survive on land.
Prokaryotic diversity
Introduction
"Perhaps bacteria may tentatively be regarded as biochemical experiments;
owing to their relatively small size and rapid growth, variations must arise
much more frequently than in more differentiated forms of life, and they
can in addition afford to occupy more precarious positions in natural
economy than larger organisms with more exacting requirements." Marjory
Stephenson, in Bacterial Metabolism, (1930)
Prokaryotic Diversity
Prokaryotes are ubiquitous, and, as mentioned above, highly diverse in their
metabolic activities. They cover every imaginable surface where there is
sufficient moisture, and they live on and inside of other living things. In the
typical human body, prokaryotic cells outnumber human body cells by
about ten to one. They comprise the majority of living things in all
ecosystems. Some prokaryotes thrive in environments that are inhospitable
for most living things. Prokaryotes recycle nutrients—essential substances
(such as carbon and nitrogen)—and they drive the evolution of new
ecosystems, some of which are natural and others man-made. Prokaryotes
have been on Earth since long before multicellular life appeared.
Prokaryotes, the First Inhabitants of Earth
When and where did life begin? What were the conditions on Earth when
life began? Prokaryotes were the first forms of life on Earth, and they
existed for billions of years before plants and animals appeared. The Earth
and its moon are thought to be about 4.54 billion years old. This estimate is
based on evidence from radiometric dating of meteorite material together
with other substrate material from Earth and the moon. Early Earth had a
very different atmosphere (contained less molecular oxygen) than it does
today and was subjected to strong radiation; thus, the first organisms would
have flourished where they were more protected, such as in ocean depths or
beneath the surface of the Earth. At this time too, strong volcanic activity
was common on Earth, so it is likely that these first organisms—the first
prokaryotes—were adapted to very high temperatures. Early Earth was
prone to geological upheaval and volcanic eruption, and was subject to
bombardment by mutagenic radiation from the sun. The first organisms
were prokaryotes that could withstand these harsh conditions.
Microbial Mats
Microbial mats or large biofilms may represent the earliest forms of life on
Earth; there is fossil evidence of their presence starting about 3.5 billion
years ago. A microbial mat is a multi-layered sheet of prokaryotes ((link])
that includes mostly bacteria, but also archaea. Microbial mats are a few
centimeters thick, and they typically grow where different types of
materials interface, mostly on moist surfaces. The various types of
prokaryotes that comprise them carry out different metabolic pathways, and
that is the reason for their various colors. Prokaryotes in a microbial mat are
held together by a glue-like sticky substance that they secrete called
extracellular matrix.
The first microbial mats likely obtained their energy from chemicals found
near hydrothermal vents. A hydrothermal vent is a breakage or fissure in
the Earth’s surface that releases geothermally heated water. With the
evolution of photosynthesis about 3 billion years ago, some prokaryotes in
microbial mats came to use a more widely available energy source—
sunlight—whereas others were still dependent on chemicals from
hydrothermal vents for energy and food.
This (a) microbial mat, about one meter in
diameter, grows over a hydrothermal vent in
the Pacific Ocean in a region known as the
“Pacific Ring of Fire.” The mat helps retain
microbial nutrients. Chimneys such as the
one indicated by the arrow allow gases to
escape. (b) In this micrograph, bacteria are
visualized using fluorescence microscopy.
(credit a: modification of work by Dr. Bob
Embley, NOAA PMEL, Chief Scientist;
credit b: modification of work by Ricardo
Murga, Rodney Donlan, CDC; scale-bar
data from Matt Russell)
Stromatolites
Fossilized microbial mats represent the earliest record of life on Earth. A
stromatolite is a sedimentary structure formed when minerals precipitate
out of water by prokaryotes in a microbial mat ({link]). Stromatolites form
layered rocks made of carbonate or silicate. Although most stromatolites are
artifacts from the past, there are places on Earth where stromatolites are still
forming. For example, growing stromatolites have been found in the Anza-
Borrego Desert State Park in San Diego County, California.
(a) These living stromatolites are located in Shark
Bay, Australia. (b) These fossilized stromatolites,
found in Glacier National Park, Montana, are
nearly 1.5 billion years old. (credit a: Robert
Young; credit b: P. Carrara, NPS)
The Ancient Atmosphere
Evidence indicates that during the first two billion years of Earth’s
existence, the atmosphere was anoxic, meaning that there was no molecular
oxygen. Therefore, only those organisms that can grow without oxygen—
anaerobic organisms—were able to live. Autotrophic organisms that
convert solar energy into chemical energy are called phototrophs, and they
appeared within one billion years of the formation of Earth. Then,
cyanobacteria, also known as blue-green algae, evolved from these simple
phototrophs one billion years later. Cyanobacteria ((link]) began the
oxygenation of the atmosphere. Increased atmospheric oxygen allowed the
development of more efficient O5-utilizing catabolic pathways. It also
opened up the land to increased colonization, because some O, is converted
into O3 (ozone) and ozone effectively absorbs the ultraviolet light that
would otherwise cause lethal mutations in DNA. Ultimately, the increase in
O» concentrations allowed the evolution of other life forms.
This hot spring in Yellowstone
National Park flows toward the
foreground. Cyanobacteria in
the spring are green, and as
water flows down the gradient,
the intensity of the color
increases as cell density
increases. The water is cooler at
the edges of the stream than in
the center, causing the edges to
appear greener. (credit: Graciela
Brelles-Marino)
Microbes Are Adaptable: Life in Moderate and Extreme
Environments
Some organisms have developed strategies that allow them to survive harsh
conditions. Prokaryotes thrive in a vast array of environments: Some grow
in conditions that would seem very normal to us, whereas others are able to
thrive and grow under conditions that would kill a plant or animal. Almost
all prokaryotes have a cell wall, a protective structure that allows them to
survive in both hyper- and hypo-osmotic conditions. Some soil bacteria are
able to form endospores that resist heat and drought, thereby allowing the
organism to survive until favorable conditions recur. These adaptations,
along with others, allow bacteria to be the most abundant life form in all
terrestrial and aquatic ecosystems.
Other bacteria and archaea are adapted to grow under extreme conditions
and are called extremophiles, meaning “lovers of extremes.”
Extremophiles have been found in all kinds of environments: the depth of
the oceans, hot springs, the Artic and the Antarctic, in very dry places, deep
inside Earth, in harsh chemical environments, and in high radiation
environments ({link]), just to mention a few. These organisms give us a
better understanding of prokaryotic diversity and open up the possibility of
finding new prokaryotic species that may lead to the discovery of new
therapeutic drugs or have industrial applications. Because they have
specialized adaptations that allow them to live in extreme conditions, many
extremophiles cannot survive in moderate environments. There are many
different groups of extremophiles: They are identified based on the
conditions in which they grow best, and several habitats are extreme in
multiple ways. For example, a soda lake is both salty and alkaline, so
organisms that live in a soda lake must be both alkaliphiles and halophiles
({link]). Other extremophiles, like radioresistant organisms, do not prefer
an extreme environment (in this case, one with high levels of radiation), but
have adapted to survive in it ({link]).
Extremophiles and Their Preferred Conditions
Extremophile Type Conditions for Optimal Growth
Acidophiles pH 3 or below
Alkaliphiles pH 9 or above
Thermophiles Temperature 60—80 °C (140-176 °F)
Hyperthermophiles Temperature 80—122 °C (176-250 °F)
Psychrophiles Temperature of -15 °C (5 °F) or lower
Halophiles Salt concentration of at least 0.2 M
Osmophiles High sugar concentration
Deinococcus
radiodurans, visualized
in this false color
transmission electron
micrograph, is a
prokaryote that can
tolerate very high doses
of ionizing radiation. It
has developed DNA
repair mechanisms that
allow it to reconstruct its
chromosome even if it
has been broken into
hundreds of pieces by
radiation or heat. (credit:
modification of work by
Michael Daly; scale-bar
data from Matt Russell)
The Ecology of Biofilms
Until a couple of decades ago, microbiologists used to think of prokaryotes
as isolated entities living apart. This model, however, does not reflect the
true ecology of prokaryotes, most of which prefer to live in communities
where they can interact. A biofilm is a microbial community (({link]) held
together in a gummy-textured matrix that consists primarily of
polysaccharides secreted by the organisms, together with some proteins and
nucleic acids. Biofilms grow attached to surfaces. Some of the best-studied
biofilms are composed of prokaryotes, although fungal biofilms have also
been described as well as some composed of a mixture of fungi and
bacteria.
Biofilms are present almost everywhere: they can cause the clogging of
pipes and readily colonize surfaces in industrial settings. In recent, large-
scale outbreaks of bacterial contamination of food, biofilms have played a
major role. They also colonize household surfaces, such as kitchen
counters, cutting boards, sinks, and toilets, as well as places on the human
body, such as the surfaces of our teeth.
Interactions among the organisms that populate a biofilm, together with
their protective exopolysaccharidic (EPS) environment, make these
communities more robust than free-living, or planktonic, prokaryotes. The
sticky substance that holds bacteria together also excludes most antibiotics
and disinfectants, making biofilm bacteria hardier than their planktonic
counterparts. Overall, biofilms are very difficult to destroy because they are
resistant to many common forms of sterilization.
Note:
Five stages of biofilm development
are shown. During stage 1, initial
attachment, bacteria adhere to a solid
surface via weak van der Waals
interactions. During stage 2,
irreversible attachment, hairlike
appendages called pili permanently
anchor the bacteria to the surface.
During stage 3, maturation I, the
biofilm grows through cell division
and recruitment of other bacteria. An
extracellular matrix composed
primarily of polysaccharides holds the
biofilm together. During stage 4,
maturation II, the biofilm continues to
grow and takes on a more complex
shape. During stage 5, dispersal, the
biofilm matrix is partly broken down,
allowing some bacteria to escape and
colonize another surface. Micrographs
of a Pseudomonas aeruginosa biofilm
in each of the stages of development
are shown. (credit: D. Davis, Don
Monroe, PLoS)
Bacterial Diseases in Humans
Devastating pathogen-borne diseases and plagues, both viral and bacterial
in nature, have affected humans since the beginning of human history. The
true cause of these diseases was not understood at the time, and some
people thought that diseases were a spiritual punishment. Over time, people
came to realize that staying apart from afflicted persons, and disposing of
the corpses and personal belongings of victims of illness, reduced their own
chances of getting sick. [link] below lists the disease and known associated
bacterial cause.
Disease Bacterium
Anthrax Bacillus anthracis
Botulism Clostridium botulinum
Chlamydia Chlamydia trachomatis
Plague Yersinia pestis
Tuberculosis Mycobacterium tuberculosis
Peptic ulcers Helicobacter pylori
Cholera Vibrio cholerae
Lyme disease Borrelia burgdorferi
Human Disease and associated bacterium
Epidemiologists study how diseases affect a population. An epidemic is a
disease that occurs in an unusually high number of individuals in a
population at the same time. A pandemic is a widespread, usually
worldwide, epidemic. An endemic disease is a disease that is constantly
present, usually at low incidence, in a population.
Long History of Bacterial Disease
There are records about infectious diseases as far back as 3000 B.C. A
number of significant pandemics caused by bacteria have been documented
over several hundred years. Some of the most memorable pandemics led to
the decline of cities and nations.
In the 21°' century, infectious diseases remain among the leading causes of
death worldwide, despite advances made in medical research and treatments
in recent decades. A disease spreads when the pathogen that causes it is
passed from one person to another. For a pathogen to cause disease, it must
be able to reproduce in the host’s body and damage the host in some way.
The Plague of Athens
In 430 B.C., the Plague of Athens killed one-quarter of the Athenian troops
that were fighting in the great Peloponnesian War and weakened Athens’
dominance and power. The plague impacted people living in overcrowded
Athens as well as troops aboard ships that had to return to Athens. The
source of the plague may have been identified recently when researchers
from the University of Athens were able to use DNA from teeth recovered
from a mass grave. The scientists identified nucleotide sequences from a
pathogenic bacterium, Salmonella enterica serovar Typhi ({link]), which
causes typhoid fever, !2o™2te] This disease is commonly seen in
overcrowded areas and has caused epidemics throughout recorded history.
Papagrigorakis MJ, Synodinos PN, and Yapijakis C. Ancient typhoid
epidemic reveals possible ancestral strain of Salmonella enterica serovar
Typhi. Infect Genet Evol 7 (2007): 126—7, Epub 2006 Jun.
Salmonella enterica serovar
Typhi, the causative agent of
Typhoid fever, is a Gram-negative,
rod-shaped gamma
protobacterium. Typhoid fever,
which is spread through feces,
causes intestinal hemorrhage, high
fever, delirium and dehydration.
Today, between 16 and 33 million
cases of this re-emerging disease
occur annually, resulting in over
200,000 deaths. Carriers of the
disease can be asymptomatic. In a
famous case in the early 1900s, a
cook named Mary Mallon
unknowingly spread the disease to
over fifty people, three of whom
died. Other Salmonella serotypes
cause food poisoning. (credit:
modification of work by NCI,
CDC)
Bubonic Plagues
From 541 to 750, an outbreak of what was likely a bubonic plague (the
Plague of Justinian), eliminated one-quarter to one-half of the human
population in the eastern Mediterranean region. The population in Europe
dropped by 50 percent during this outbreak. Bubonic plague would strike
Europe more than once.
One of the most devastating pandemics was the Black Death (1346 to
1361) that is believed to have been another outbreak of bubonic plague
caused by the bacterium Yersinia pestis. It is thought to have been
contracted initially in China and spread along the Silk Road, a network of
land and sea trade routes, to the Mediterranean region and Europe, carried
by rat fleas living on black rats that were always present on ships. The
Black Death reduced the world’s population from an estimated 450 million
to about 350 to 375 million. Bubonic plague struck London hard again in
the mid-1600s ({link]). In modern times, approximately 1,000 to 3,000
cases of plague arise globally each year. Although contracting bubonic
plague before antibiotics meant almost certain death, the bacterium
responds to several types of modern antibiotics, and mortality rates from
plague are now very low.
The (a) Great Plague of London killed an
estimated 200,000 people, or about twenty percent
of the city’s population. The causative agent, the
(b) bacterium Yersinia pestis, is a Gram-negative,
rod-shaped bacterium from the class Gamma
Proteobacteria. The disease is transmitted through
the bite of an infected flea, which is infected by a
rodent. Symptoms include swollen lymph nodes,
fever, seizure, vomiting of blood, and (c)
gangrene. (credit b: Rocky Mountain
Laboratories, NIAID, NIH; scale-bar data from
Matt Russell; credit c: Textbook of Military
Medicine, Washington, D.C., U.S. Dept. of the
Army, Office of the Surgeon General, Borden
Institute)
Migration of Diseases to New Populations
Over the centuries, Europeans tended to develop genetic immunity to
endemic infectious diseases, but when European conquerors reached the
western hemisphere, they brought with them disease-causing bacteria and
viruses, which triggered epidemics that completely devastated populations
of Native Americans, who had no natural resistance to many European
diseases. It has been estimated that up to 90 percent of Native Americans
died from infectious diseases after the arrival of Europeans, making
conquest of the New World a foregone conclusion.
Emerging and Re-emerging Diseases
The distribution of a particular disease is dynamic. Therefore, changes in
the environment, the pathogen, or the host population can dramatically
impact the spread of a disease. According to the World Health Organization
(WHO) an emerging disease ([link]) is one that has appeared in a
population for the first time, or that may have existed previously but is
rapidly increasing in incidence or geographic range. This definition also
includes re-emerging diseases that were previously under control.
Approximately 75 percent of recently emerging infectious diseases
affecting humans are zoonotic diseases, zoonoses, diseases that primarily
infect animals and are transmitted to humans; some are of viral origin and
some are of bacterial origin. Brucellosis is an example of a prokaryotic
zoonosis that is re-emerging in some regions, and necrotizing fasciitis
(commonly known as flesh-eating bacteria) has been increasing in virulence
for the last 80 years for unknown reasons.
Vancomycin-resistant Multidrug-resistant
Staphylococcus aureus tuberculosis
The map shows regions where bacterial
diseases are emerging or reemerging. (credit:
modification of work by NIH)
Some of the present emerging diseases are not actually new, but are
diseases that were catastrophic in the past ([link]). They devastated
populations and became dormant for a while, just to come back, sometimes
more virulent than before, as was the case with bubonic plague. Other
diseases, like tuberculosis, were never eradicated but were under control in
some regions of the world until coming back, mostly in urban centers with
high concentrations of immunocompromised people. The WHO has
identified certain diseases whose worldwide re-emergence should be
monitored. Among these are two viral diseases (dengue fever and yellow
fever), and three prokaryotic diseases (diphtheria, cholera, and bubonic
plague). The war against infectious diseases has no foreseeable end.
Life Cycle of the Ixodes scapularis Tick
0 reeds once, Yy
(Deer is preferred host) 2
Spring 3 weeks i ¢ {\ o Fall
IN
Nymph Yer Deposited
Egg. © —@aduts die
Feeds once, 3-4 days ff
1 month (Mouse is preferred host)
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Summer
(a) (c)
Lyme disease often, but not always, results in (a) a
characteristic bullseye rash. The disease is caused
by a (b) Gram-negative spirochete bacterium of
the genus Borellia. The bacteria (c) infect ticks,
which in turns infect mice. Deer are the preferred
secondary host, but the ticks also may feed on
humans. Untreated, the disease causes chronic
disorders in the nervous system, eyes, joints, and
heart. The disease is named after Lyme,
Connecticut, where an outbreak occurred in 1995
and has subsequently spread. The disease is not
new, however. Genetic evidence suggests that Otzi
the Iceman, a 5,300-year-old mummy found in the
Alps, was infected with Borellia. (credit a: James
Gathany, CDC; credit b: CDC; scale-bar data from
Matt Russell)
Biofilms and Disease
Recall that biofilms are microbial communities that are very difficult to
destroy. They are responsible for diseases such as infections in patients with
cystic fibrosis, Legionnaires’ disease, and otitis media. They produce dental
plaque and colonize catheters, prostheses, transcutaneous and orthopedic
devices, contact lenses, and internal devices such as pacemakers. They also
form in open wounds and burned tissue. In healthcare environments,
biofilms grow on hemodialysis machines, mechanical ventilators, shunts,
and other medical equipment. In fact, 65 percent of all infections acquired
in the hospital (nosocomial infections) are attributed to biofilms. Biofilms
are also related to diseases contracted from food because they colonize the
surfaces of vegetable leaves and meat, as well as food-processing
equipment that isn’t adequately cleaned.
Biofilm infections develop gradually; sometimes, they do not cause
symptoms immediately. They are rarely resolved by host defense
mechanisms. Once an infection by a biofilm is established, it is very
difficult to eradicate, because biofilms tend to be resistant to most of the
methods used to control microbial growth, including antibiotics. Biofilms
respond poorly or only temporarily to antibiotics; it has been said that they
can resist up to 1,000 times the antibiotic concentrations used to kill the
same bacteria when they are free-living or planktonic. An antibiotic dose
that large would harm the patient; therefore, scientists are working on new
ways to get rid of biofilms.
Antibiotics: Are We Facing a Crisis?
The word antibiotic comes from the Greek anti meaning “against” and bios
meaning “life.” An antibiotic is a chemical, produced either by microbes or
synthetically, that is hostile to the growth of other organisms. Today’s news
and media often address concerns about an antibiotic crisis. Are the
antibiotics that easily treated bacterial infections in the past becoming
obsolete? Are there new “superbugs”—bacteria that have evolved to
become more resistant to our arsenal of antibiotics? Is this the beginning of
the end of antibiotics? All these questions challenge the healthcare
community.
One of the main causes of resistant bacteria is the abuse of antibiotics. The
imprudent and excessive use of antibiotics has resulted in the natural
selection of resistant forms of bacteria. The antibiotic kills most of the
infecting bacteria, and therefore only the resistant forms remain. These
resistant forms reproduce, resulting in an increase in the proportion of
resistant forms over non-resistant ones. Another major misuse of antibiotics
is in patients with colds or the flu, for which antibiotics are useless. Another
problem is the excessive use of antibiotics in livestock. The routine use of
antibiotics in animal feed promotes bacterial resistance as well. In the
United States, 70 percent of the antibiotics produced are fed to animals.
These antibiotics are given to livestock in low doses, which maximize the
probability of resistance developing, and these resistant bacteria are readily
transferred to humans.
One of the Superbugs: MRSA
The imprudent use of antibiotics has paved the way for bacteria to expand
populations of resistant forms. For example, Staphylococcus aureus, often
called “staph,” is a common bacterium that can live in the human body and
is usually easily treated with antibiotics. A very dangerous strain, however,
methicillin-resistant Staphylococcus aureus (MRSA) has made the news
over the past few years ((link]). This strain is resistant to many commonly
used antibiotics, including methicillin, amoxicillin, penicillin, and oxacillin.
MRSA can cause infections of the skin, but it can also infect the
bloodstream, lungs, urinary tract, or sites of injury. While MRSA infections
are common among people in healthcare facilities, they have also appeared
in healthy people who haven’t been hospitalized but who live or work in
tight populations (like military personnel and prisoners). Researchers have
expressed concern about the way this latter source of MRSA targets a much
younger population than those residing in care facilities. The Journal of the
American Medical Association reported that, among MRSA-afflicted
persons in healthcare facilities, the average age is 68, whereas people with
“community-associated MRSA” (CA-MRSA) have an average age of 23.
[footnote]
Naimi, TS, LeDell, KH, Como-Sabetti, K, et al. Comparison of community-
and health care-associated methicillin-resistant Staphylococcus aureus
infection. JAMA 290 (2003): 2976-84, doi: 10.1001/jama.290.22.2976.
This scanning electron
micrograph shows methicillin-
resistant Staphylococcus aureus
bacteria, commonly known as
MRSA. S. Aureus is not always
pathogenic, but can cause
diseases such as food poisoning
and skin and respiratory
infections. (credit: modification
of work by Janice Haney Carr;
scale-bar data from Matt
Russell)
In summary, the medical community is facing an antibiotic crisis. Some
scientists believe that after years of being protected from bacterial
infections by antibiotics, we may be returning to a time in which a simple
bacterial infection could again devastate the human population. Researchers
are developing new antibiotics, but it takes many years to of research and
clinical trials, plus financial investments in the millions of dollars, to
generate an effective and approved drug.
Foodborne Diseases
Prokaryotes are everywhere: They readily colonize the surface of any type
of material, and food is not an exception. Most of the time, prokaryotes
colonize food and food-processing equipment in the form of a biofilm.
Outbreaks of bacterial infection related to food consumption are common.
A foodborne disease (colloquially called “food poisoning”) is an illness
resulting from the consumption of contaminated food, or the pathogenic
bacteria, viruses, or other parasites that contaminate food. Although the
United States has one of the safest food supplies in the world, the U.S.
Centers for Disease Control and Prevention (CDC) has reported that “76
million people get sick, more than 300,000 are hospitalized, and 5,000
Americans die each year from foodborne illness.”
The characteristics of foodborne illnesses have changed over time. In the
past, it was relatively common to hear about sporadic cases of botulism, the
potentially fatal disease produced by a toxin from the anaerobic bacterium
Clostridium botulinum. Some of the most common sources for this
bacterium were non-acidic canned foods, homemade pickles, and processed
meat and sausages. The can, jar, or package created a suitable anaerobic
environment where Clostridium could grow. Proper sterilization and
canning procedures have reduced the incidence of this disease.
While people may tend to think of foodborne illnesses as associated with
animal-based foods, most cases are now linked to produce. There have been
serious, produce-related outbreaks associated with raw spinach in the
United States and with vegetable sprouts in Germany, and these types of
outbreaks have become more common. The raw spinach outbreak in 2006
was produced by the bacterium E. coli serotype O157:H7. A serotype is a
strain of bacteria that carries a set of similar antigens on its cell surface, and
there are often many different serotypes of a bacterial species. Most E. coli
are not particularly dangerous to humans, but serotype 0157:H7 can cause
bloody diarrhea and is potentially fatal.
All types of food can potentially be contaminated with bacteria. Recent
outbreaks of Salmonella reported by the CDC occurred in foods as diverse
as peanut butter, alfalfa sprouts, and eggs. A deadly outbreak in Germany in
2010 was caused by E. coli contamination of vegetable sprouts ({link]). The
strain that caused the outbreak was found to be a new serotype not
previously involved in other outbreaks, which indicates that E. coli is
continuously evolving.
(a) Vegetable sprouts grown at an organic farm were
the cause of an (b) EF. coli outbreak that killed 32
people and sickened 3,800 in Germany in 2011. The
strain responsible, E. coli 0104:H4, produces Shiga
toxin, a substance that inhibits protein synthesis in the
host cell. The toxin (c) destroys red blood cells
resulting in bloody diarrhea. Deformed red blood
cells clog the capillaries of the kidney, which can lead
to kidney failure, as happened to 845 patients in the
2011 outbreak. Kidney failure is usually reversible,
but some patients experience kidney problems years
later. (credit c: NIDDK, NIH)
Note:
Career Connection
Epidemiologist
Epidemiology is the study of the occurrence, distribution, and determinants
of health and disease in a population. It is, therefore, part of public health.
An epidemiologist studies the frequency and distribution of diseases within
human populations and environments.
Epidemiologists collect data about a particular disease and track its spread
to identify the original mode of transmission. They sometimes work in
close collaboration with historians to try to understand the way a disease
evolved geographically and over time, tracking the natural history of
pathogens. They gather information from clinical records, patient
interviews, surveillance, and any other available means. That information
is used to develop strategies, such as vaccinations ([link]), and design
public health policies to reduce the incidence of a disease or to prevent its
spread. Epidemiologists also conduct rapid investigations in case of an
outbreak to recommend immediate measures to control it.
An epidemiologist has a bachelor’s degree, plus a master’s degree in public
health (MPH). Many epidemiologists are also physicians (and have an
M.D.), or they have a Ph.D. in an associated field, such as biology or
microbiology.
Vaccinations can slow the spread of
communicable diseases. (credit:
modification of work by Daniel
Paquet)
Beneficial Bacteria
Not all prokaryotes are pathogenic. On the contrary, pathogens represent
only a very small percentage of the diversity of the microbial world. In fact,
our life would not be possible without prokaryotes. Just think about the role
of prokaryotes in biogeochemical cycles.
Cooperation between Bacteria and Eukaryotes: Nitrogen
Fixation
Nitrogen is a very important element to living things, because it is part of
nucleotides and amino acids that are the building blocks of nucleic acids
and proteins, respectively. Nitrogen is usually the most limiting element in
terrestrial ecosystems, with atmospheric nitrogen, N>, providing the largest
pool of available nitrogen. However, eukaryotes cannot use atmospheric,
gaseous nitrogen to synthesize macromolecules. Fortunately, nitrogen can
be “fixed,” meaning it is converted into ammonia (NH3) either biologically
or abiotically. Abiotic nitrogen fixation occurs as a result of lightning or by
industrial processes.
Biological nitrogen fixation (BNF) is exclusively carried out by
prokaryotes: soil bacteria, cyanobacteria, and Frankia spp. (filamentous
bacteria interacting with actinorhizal plants such as alder, bayberry, and
sweet fern). After photosynthesis, BNF is the second most important
biological process on Earth. The equation representing the process is as
follows
Equation:
N.+16ATP + 8e + 8H* — 2NH;+ 16ADP + 16Pi+ H,
where Pi stands for inorganic phosphate. The total fixed nitrogen through
BNF is about 100 to 180 million metric tons per year. Biological processes
contribute 65 percent of the nitrogen used in agriculture.
Cyanobacteria are the most important nitrogen fixers in aquatic
environments. In soil, members of the genus Clostridium are examples of
free-living, nitrogen-fixing bacteria. Other bacteria live symbiotically with
legume plants, providing the most important source of BNF. Symbionts
may fix more nitrogen in soils than free-living organisms by a factor of 10.
Soil bacteria, collectively called rhizobia, are able to symbiotically interact
with legumes to form nodules, specialized structures where nitrogen
fixation occurs ({link]). Nitrogenase, the enzyme that fixes nitrogen, is
inactivated by oxygen, so the nodule provides an oxygen-free area for
nitrogen fixation to take place. This process provides a natural and
inexpensive plant fertilizer, as it reduces atmospheric nitrogen into
ammonia, which is easily usable by plants. The use of legumes is an
excellent alternative to chemical fertilization and is of special interest to
sustainable agriculture, which seeks to minimize the use of chemicals and
conserve natural resources. Through symbiotic nitrogen fixation, the plant
benefits from using an endless source of nitrogen: the atmosphere. Bacteria
benefit from using photosynthates (carbohydrates produced during
photosynthesis) from the plant and having a protected niche. Additionally,
the soil benefits from being naturally fertilized. Therefore, the use of
rhizobia as biofertilizers is a sustainable practice.
Why are legumes so important? Some, like soybeans, are key sources of
agricultural protein. Some of the most important grain legumes are soybean,
peanuts, peas, chickpeas, and beans. Other legumes, such as alfalfa, are
used to feed cattle.
Soybean (Glycine max) is a
legume that interacts
symbiotically with the soil
bacterium Bradyrhizobium
japonicum to form specialized
structures on the roots called
nodules where nitrogen fixation
occurs. (credit: USDA)
Early Biotechnology: Cheese, Bread, Wine, Beer, and Yogurt
According to the United Nations Convention on Biological Diversity,
biotechnology is “any technological application that uses biological
systems, living organisms, or derivatives thereof, to make or modify
products or processes for specific use."!#22™°'e] The concept of “specific
use” involves some sort of commercial application. Genetic engineering,
artificial selection, antibiotic production, and cell culture are current topics
of study in biotechnology. However, humans have used prokaryotes before
the term biotechnology was even coined. In addition, some of the goods and
services are as simple as cheese, bread, wine, beer, and yogurt, which
employ both bacteria and other microbes, such as yeast, a fungus ([link]).
http://www.cbd.int/convention/articles/?a=cbd-02, United Nations
Convention on Biological Diversity: Article 2: Use of Terms.
Some of the products derived from the use of
prokaryotes in early biotechnology include (a)
cheese, (b) wine, (c) beer and bread, and (d) yogurt.
(credit bread: modification of work by F.
Rodrigo/Wikimedia Commons; credit wine:
modification of work by Jon Sullivan; credit beer
and bread: modification of work by Kris Miller;
credit yogurt: modification of work by Jon
Sullivan)
Cheese production began around 4,000—7,000 years ago when humans
began to breed animals and process their milk. Fermentation in this case
preserves nutrients: Milk will spoil relatively quickly, but when processed
as cheese, it is more stable. As for beer, the oldest records of brewing are
about 6,000 years old and refer to the Sumerians. Evidence indicates that
the Sumerians discovered fermentation by chance. Wine has been produced
for about 4,500 years, and evidence suggests that cultured milk products,
like yogurt, have existed for at least 4,000 years.
Using Prokaryotes to Clean up Our Planet: Bioremediation
Microbial bioremediation is the use of prokaryotes (or microbial
metabolism) to remove pollutants. Bioremediation has been used to remove
agricultural chemicals (pesticides, fertilizers) that leach from soil into
groundwater and the subsurface. Certain toxic metals and oxides, such as
selenium and arsenic compounds, can also be removed from water by
bioremediation. The reduction of SeO,°* to SeO3"2 and to Se® (metallic
selenium) is a method used to remove selenium ions from water. Mercury is
an example of a toxic metal that can be removed from an environment by
bioremediation. As an active ingredient of some pesticides, mercury is used
in industry and is also a by-product of certain processes, such as battery
production. Methyl mercury is usually present in very low concentrations in
natural environments, but it is highly toxic because it accumulates in living
tissues. Several species of bacteria can carry out the biotransformation of
toxic mercury into nontoxic forms. These bacteria, such as Pseudomonas
aeruginosa, can convert Hg*? into Hg®, which is nontoxic to humans.
One of the most useful and interesting examples of the use of prokaryotes
for bioremediation purposes is the cleanup of oil spills. The importance of
prokaryotes to petroleum bioremediation has been demonstrated in several
oil spills in recent years, such as the Exxon Valdez spill in Alaska (1989)
({link]), the Prestige oil spill in Spain (2002), the spill into the
Mediterranean from a Lebanon power plant (2006), and more recently, the
BP oil spill in the Gulf of Mexico (2010). To clean up these spills,
bioremediation is promoted by the addition of inorganic nutrients that help
bacteria to grow. Hydrocarbon-degrading bacteria feed on hydrocarbons in
the oil droplet, breaking down the hydrocarbons. Some species, such as
Alcanivorax borkumensis, produce surfactants that solubilize the oil,
whereas other bacteria degrade the oil into carbon dioxide. In the case of oil
spills in the ocean, ongoing, natural bioremediation tends to occur,
inasmuch as there are oil-consuming bacteria in the ocean prior to the spill.
In addition to naturally occurring oil-degrading bacteria, humans select and
engineer bacteria that possess the same capability with increased efficacy
and spectrum of hydrocarbon compounds that can be processed. Under
ideal conditions, it has been reported that up to 80 percent of the nonvolatile
components in oil can be degraded within one year of the spill. Other oil
fractions containing aromatic and highly branched hydrocarbon chains are
more difficult to remove and remain in the environment for longer periods
of time.
(b)
(a) Cleaning up oil after the Valdez spill in Alaska,
workers hosed oil from beaches and then used a
floating boom to corral the oil, which was finally
skimmed from the water surface. Some species of
bacteria are able to solubilize and degrade the oil. (b)
One of the most catastrophic consequences of oil
spills is the damage to fauna. (credit a: modification
of work by NOAA; credit b: modification of work by
GOLUBENKOV, NGO: Saving Taman)
Note:
Everyday Connection
Microbes on the Human Body
The commensal bacteria that inhabit our skin and gastrointestinal tract do a
host of good things for us. They protect us from pathogens, help us digest
our food, and produce some of our vitamins and other nutrients. These
activities have been known for a long time. More recently, scientists have
gathered evidence that these bacteria may also help regulate our moods,
influence our activity levels, and even help control weight by affecting our
food choices and absorption patterns. The Human Microbiome Project has
begun the process of cataloging our normal bacteria (and archaea) so we
can better understand these functions.
A particularly fascinating example of our normal flora relates to our
digestive systems. People who take high numbers of antibiotics tend to lose
many of their normal gut bacteria, allowing a naturally antibiotic-resistant
species called Clostridium difficile to overgrow and cause severe gastric
problems, especially chronic diarrhea ([link]). Obviously, trying to treat
this problem with antibiotics only makes it worse. However, it has been
successfully treated by giving the patients fecal transplants from healthy
donors to reestablish the normal intestinal microbial community. Clinical
trials are underway to ensure the safety and effectiveness of this technique.
This scanning electron micrograph
shows Clostridium difficile, a
Gram-positive, rod-shaped
bacterium that causes severe
diarrhea. Infection commonly
occurs after the normal gut fauna is
eradicated by antibiotics. (credit:
modification of work by CDC,
HHS; scale-bar data from Matt
Russell)
Scientists are also discovering that the absence of certain key microbes
from our intestinal tract may set us up for a variety of problems. This
seems to be particularly true regarding the appropriate functioning of the
immune system. There are intriguing findings that suggest that the absence
of these microbes is an important contributor to the development of
allergies and some autoimmune disorders. Research is currently underway
to test whether adding certain microbes to our internal ecosystem may help
in the treatment of these problems as well as in treating some forms of
autism.
Kingdom Fungi
Introduction
"Now when you cut a forest, an ancient forest in particular, you are not just
removing a lot of big trees and a few birds fluttering around in the canopy.
You are drastically imperiling a vast array of species within a few square
miles of you. The number of these species may go to tens of thousands. ...
Many of them are still unknown to science, and science has not yet
discovered the key role undoubtedly played in the maintenance of that
ecosystem, as in the case of fungi, microorganisms, and many of the
insects." Edward O. Wilson, "On Human Nature" (2000). In John H.
Morgan, Naturally Good, (2005)
- a
(a) (b) (c)
The (a) familiar mushroom is only one type of fungus. The
brightly colored fruiting bodies of this (b) coral fungus are
displayed. This (c) electron micrograph shows the spore-
bearing structures of Aspergillus, a type of toxic fungi
found mostly in soil and plants. (credit a: modification of
work by Chris Wee; credit b: modification of work by Cory
Zanker; credit c: modification of work by Janice Haney
Carr, Robert Simmons, CDC; scale-bar data from Matt
Russell)
The word fungus comes from the Latin word for mushroom. Indeed, the
familiar mushrooms are fungi, but there are many other types of fungi as
well ((link]). The kingdom Fungi includes an enormous variety of living
organisms collectively referred to as Eumycota, or true fungi. While
scientists have identified about 100,000 species of fungi, this is only a
fraction of the over 5 million species likely present on Earth. Edible
mushrooms, yeasts, black mold, and Penicillium notatum (the producer of
the antibiotic penicillin) are all members of the kingdom Fungi, which
belongs to the domain Eukarya. As eukaryotes, a typical fungal cell
contains a true nucleus and many membrane-bound organelles.
Fungi were once considered plant-like organisms; however, DNA
comparisons have shown that fungi are more closely related to animals than
plants. Fungi are not capable of photosynthesis: They use complex organic
compounds as sources of energy and carbon. Some fungal organisms
multiply only asexually, whereas others undergo both asexual reproduction
and sexual reproduction. Most fungi produce a large number of spores that
are disseminated by the wind. Like bacteria, fungi play an essential role in
ecosystems, because they are decomposers and participate in the cycling of
nutrients by breaking down organic materials into simple molecules.
Fungi often interact with other organisms, forming mutually beneficial or
mutualistic associations. Fungi also cause serious infections in plants and
animals. For example, Dutch elm disease is a particularly devastating
fungal infection that destroys many native species of elm (Ulmus spp.). The
fungus infects the vascular system of the tree. It was accidentally
introduced to North America in the 1900s and decimated elm trees across
the continent. Dutch elm disease is caused by the fungus Ophiostoma ulmi.
The elm bark beetle acts as a vector and transmits the disease from tree to
tree. Many European and Asiatic elms are less susceptible than American
elms.
In humans, fungal infections are generally considered challenging to treat
because, unlike bacteria, they do not respond to traditional antibiotic
therapy since they are also eukaryotes. These infections may prove deadly
for individuals with a compromised immune system.
Fungi have many commercial applications. The food industry uses yeasts in
baking, brewing, and wine making. Many industrial compounds are
byproducts of fungal fermentation. Fungi are the source of many
commercial enzymes and antibiotics.
Cell Structure and Function
Fungi are eukaryotes and as such have a complex cellular organization. As
eukaryotes, fungal cells contain a membrane-bound nucleus. A few types of
fungi have structures comparable to the plasmids (loops of DNA) seen in
bacteria. Fungal cells also contain mitochondria and a complex system of
internal membranes, including the endoplasmic reticulum and Golgi
apparatus.
Fungal cells do not have chloroplasts. Although the photosynthetic pigment
chlorophyll is absent, many fungi display bright colors, ranging from red to
green to black. The poisonous Amanita muscaria (fly agaric) is
recognizable by its bright red cap with white patches ([link]). Pigments in
fungi are associated with the cell wall and play a protective role against
ultraviolet radiation. Some pigments are toxic.
The poisonous Amanita muscaria
is native to the temperate and
boreal regions of North America.
(credit: Christine Majul)
Like plant cells, fungal cells are surrounded by a thick cell wall; however,
the rigid layers contain the complex polysaccharides chitin and glucan.
Cellulose, the main component of plant cell walls, is found rarely in fungi.
Chitin, also found in the exoskeleton of insects, gives structural strength to
the cell walls of fungi. The cell wall protects the cell from desiccation and
predators. Similar to plants, some fungi contain a large central vacuole. The
large central vacuole permits growth without spending many resources on
regenerating the expensive cytoplasm. Fungi have plasma membranes
similar to other eukaryotes, except that the structure is stabilized by
ergosterol, a steroid molecule that functions like the cholesterol found in
animal plasma membranes. Most members of the kingdom Fungi are
nonmotile. Flagella are produced only by the gametes in the primitive
division Chytridiomycota.
Growth
The vegetative body of a fungus is called a thallus and can be unicellular or
multicellular. Some fungi are dimorphic because they can go from being
unicellular to multicellular depending on environmental conditions.
Unicellular fungi are generally referred to as yeasts.Saccharomyces
cerevisiae (baker’s yeast) and Candida species (the agents of thrush, a
common fungal infection) are examples of unicellular fungi.
Most fungi are multicellular organisms. They display two distinct
morphological stages: vegetative and reproductive. The vegetative stage is
characterized by a tangle of slender thread-like structures called hyphae
(singular, hypha), whereas the reproductive stage can be more conspicuous.
A mass of hyphae is called a mycelium ((link]). It can grow on a surface, in
soil or decaying material, in a liquid, or even in or on living tissue.
Although individual hypha must be observed under a microscope, the
mycelium of a fungus can be very large with some species truly being “the
fungus humongous.” The giant Armillaria ostoyae (honey mushroom) is
considered the largest organism on Earth, spreading across over 2,000 acres
of underground soil in eastern Oregon; it is estimated to be at least 2,400
years old.
The mycelium of the fungus
Neotestudina rosati can be
pathogenic to humans. The
fungus enters through a cut or
scrape and develops into a
mycetoma, a chronic
subcutaneous infection. (credit:
CDG)
Most fungal hyphae are divided into separate cells by end walls called septa
(singular, septum. In most divisions (like plants, fungal phyla are called
divisions by tradition) of fungi, tiny holes in the septa allow for the rapid
flow of nutrients and small molecules from cell to cell along the hyphae.
They are described as perforated septa. The hyphae in bread molds (which
belong to the division Zygomycota) are not separated by septa. They are
formed of large cells containing many nuclei, an arrangement described as
coenocytic hyphae.
Fungi thrive in environments that are moist and slightly acidic, and can
grow with or without light. They vary in their oxygen requirements. Most
fungi are obligate aerobes, requiring oxygen to survive. Other species, such
as the Chytridiomycota that reside in the rumen of cattle, are obligate
anaerobes, meaning that they cannot grow and reproduce in an environment
with oxygen. Yeasts are facultative: They grow best in the presence of
oxygen but can use fermentation in the absence of oxygen. The alcohol
produced from yeast fermentation is used in wine and beer production, and
the carbon dioxide they produce carbonates beer and sparkling wine, and
makes bread rise.
How Fungi Obtain Nutrition
Like animals, fungi are heterotrophs: They use complex organic compounds
as a source of carbon rather than fixing carbon dioxide from the
atmosphere, as some bacteria and most plants do. In addition, fungi do not
fix nitrogen from the atmosphere. Like animals, they must obtain it from
their diet. However, unlike most animals that ingest food and then digest it
internally in specialized organs, fungi perform these steps in the reverse
order. Digestion precedes ingestion. First, exoenzymes, enzymes that
catalyze reactions on compounds outside of the cell, are transported out of
the hyphae where they break down nutrients in the environment. Then, the
smaller molecules produced by the external digestion are absorbed through
the large surface areas of the mycelium. As with animal cells, the fungal
storage polysaccharide is glycogen rather than starch, as found in plants.
Fungi are mostly saprobes, organisms that derive nutrients from decaying
organic matter. They obtain their nutrients from dead or decomposing
organic matter, mainly plant material. Fungal exoenzymes are able to break
down insoluble polysaccharides, such as the cellulose and lignin of dead
wood, into readily absorbable glucose molecules. Decomposers are
important components of ecosystems, because they return nutrients locked
in dead bodies to a form that is usable for other organisms. This role is
discussed in more detail later. Because of their varied metabolic pathways,
fungi fulfill an important ecological role and are being investigated as
potential tools in bioremediation. For example, some species of fungi can
be used to break down diesel oil and polycyclic aromatic hydrocarbons.
Other species take up heavy metals such as cadmium and lead.
Some fungi are parasitic and use enzymes systems similar to the ones
described above to break down plant cell walls and access plant resources
within the cell. Other parasitic fungi can also penetrate the outside defenses
of animals and acquire nourishment from the organism. These fungi are
pathogenic and cause disease in the host see the pathogenic section for
more information.
Reproduction
Fungi reproduce sexually and/or asexually. When Fungi reproduce sexually,
spores are produced by meiosis, and these spores are referred to as
meiospores. Fungi can also produce spores mitosis (asexual reproduction),
and the spores produced are called mitospores. There are groups of fungi
that reproduce only using mitospores are called the mitosporic fungi.
In both sexual and asexual reproduction, fungi produce spores that disperse
from the parent organism by either floating on the wind or hitching a ride
on an animal. Fungal spores are smaller and lighter than plant seeds. The
giant puffball mushroom bursts open and releases trillions of spores. The
huge number of spores released increases the likelihood of landing in an
environment that will support growth ((Link]).
(a)
The (a) giant puff ball mushroom releases
(b) a cloud of spores when it reaches
maturity. (credit a: modification of work by
Roger Griffith; credit b: modification of
work by Pearson Scott Foresman, donated to
the Wikimedia Foundation)
Asexual Reproduction
Fungi reproduce asexually by fragmentation of the mycelium. Fragments of
hyphae can grow new colonies which are identical. The fragmentation of
mycelium maintain clonal populations adapted to a specific niche, and
allows for more rapid dispersal than sexual reproduction.
The most common mode of asexual reproduction is through the formation
of asexual spores or mitospores, which are produced by one parent only
(through mitosis) and are genetically identical to that parent ({link]). Spores
allow fungi to expand their distribution and colonize new environments.
They may be released from the parent thallus either outside or within a
specialized reproductive structure.
Fungi Life Cycle
Spores
Germination Asevial Mitosis
Reproduction
Plasmogamy: Ket cs ee
Haploid cells from = : ae ae
two diffirent mycelia CFCe) A multi-cellular
fuse to forma mycelium is formed.
heterokaryotic cell
with two or more
: Sexual g
lea in Reproduction fog Spores
Heterokaryotic
stage
Karyogamy: Meiosis:
The nuclei fuse to at, Haploid (1n) spores
form a diploid (2n) are formed.
zygote.
Fungi may have both asexual and sexual stages
of reproduction.
There are many types of mitospores. Conidiospores are unicellular or
multicellular spores that are released directly from the tip or side of the
hypha. Other mitospores originate in the fragmentation of a hypha to form
single cells that are released as spores; some of these have a thick wall
surrounding the fragment. Yet others bud off the vegetative parent cell.
Sporangiospores are produced in a sporangium ([link]).
This bright field light micrograph shows
the release of spores from a sporangium
at the end of a hypha called a
sporangiophore. The organism is a
Mucor sp. fungus, a mold often found
indoors. (credit: modification of work by
Dr. Lucille Georg, CDC; scale-bar data
from Matt Russell)
Sexual Reproduction
Sexual reproduction introduces genetic variation into a population of fungi.
In fungi, sexual reproduction often occurs in response to adverse
environmental conditions. During sexual reproduction, two mating types
are produced. When both mating types are present in the same mycelium, it
is called homothallic, or self-fertile. Heterothallic mycelia require two
different, but compatible, mycelia to reproduce sexually.
Although there are many variations in fungal sexual reproduction, all
include the following three stages ({link]). First, during cytoplasmic fusion
(plasmogamy), two haploid cells fuse, leading to a dikaryotic stage where
two haploid nuclei coexist in a single cell. During karyogamy (“nuclear
marriage”), the haploid nuclei fuse to form a diploid zygote nucleus. For
some groups of fungi, karyogamy and plasmogamy can be separated for a
long periods of time and some fungi maintain dikaryotic vegetative
mycelium. Finally, meiosis takes place in the gametangia (singular,
gametangium) organs, in which gametes of different mating types are
generated. At this stage, spores are disseminated into the environment.
Fungal Diversity
The kingdom Fungi contains five major phyla that were established
according to their mode of sexual reproduction or using molecular data.
Polyphyletic, unrelated fungi that reproduce without a sexual cycle, are
placed for convenience in a sixth group called a “form phylum”. Not all
mycologists agree with this scheme. Rapid advances in molecular biology
and the sequencing of rRNA genes continue to show new and different
relationships between the various categories of fungi ([link]). The five true
phyla of fungi are the Chytridiomycota (Chytrids), the Zygomycota
(conjugated fungi), the Ascomycota (sac fungi), the Basidiomycota (club
fungi) and the recently described Phylum Glomeromycota. The
Deuteromycota is an informal group of unrelated fungi that all share a
common character — they use strictly asexual reproduction or are called
mitosporic.
Se YX US ae
Basidiomycota Ascomycota Glomeromycota Zygomycota Chytridiomycota Animalia
A phylogenetic tree of five groups of fungi
Chytridiomycota (Chytrids), the Zygomycota
(conjugated fungi), the Ascomycota (sac fungi), the
Basidiomycota (club fungi) and the recently described
Phylum Glomeromycota. Work by Eva Horne.
Note: “-mycota” is used to designate a phylum while “-mycetes” formally
denotes a class or is used informally to refer to all members of the phylum.
Chytridiomycota: The Chytrids
The only class in the Phylum Chytridiomycota is the Chytridiomycetes.
The chytrids are the simplest and most primitive Eumycota, or true fungi.
The evolutionary record shows that the first recognizable chytrids appeared
during the late pre-Cambrian period, more than 500 million years ago. Like
all fungi, chytrids have chitin in their cell walls, but one group of chytrids
has both cellulose and chitin in the cell wall. Most chytrids are unicellular;
a few form multicellular organisms and hyphae, which have no septa
between cells (coenocytic). They produce gametes and diploid zoospores
that swim with the help of a single flagellum.
The ecological habitat and cell structure of chytrids have much in common
with protists. Chytrids usually live in aquatic environments, although some
species live on land. Some species thrive as parasites on plants, insects, or
amphibians ([link]), while others are saprobes. The chytrid species
Allomyces is well characterized as an experimental organism. Its
reproductive cycle includes both asexual and sexual phases. Allomyces
produces diploid or haploid flagellated zoospores in a sporangium.
The chytrid
Batrachochytrium
dendrobatidis is seen in these
light micrographs as
transparent spheres growing
on (a) a freshwater arthropod
and (b) algae. This chytrid
causes skin diseases in many
species of amphibians,
resulting in species decline
and extinction. (credit:
modification of work by
Johnson ML, Speare R.,
CDC)
Zygomycota: The Conjugated Fungi
The zygomycetes are a relatively small group of fungi belonging to the
Phylum Zygomycota. They include the familiar bread mold, Rhizopus
stolonifer, which rapidly propagates on the surfaces of breads, fruits, and
vegetables. Most species are saprobes, living off decaying organic material;
a few are parasites, particularly of insects. Zygomycetes play a considerable
commercial role. The metabolic products of other species of Rhizopus are
intermediates in the synthesis of semi-synthetic steroid hormones.
Zygomycetes have a thallus of coenocytic hyphae in which the nuclei are
haploid when the organism is in the vegetative stage. The fungi usually
reproduce asexually by producing sporangiospores ([link]). The black tips
of bread mold are the swollen sporangia packed with black spores ([link]).
When spores land on a suitable substrate, they germinate and produce a new
mycelium. Sexual reproduction starts when conditions become unfavorable.
Two opposing mating strains (type + and type —) must be in close proximity
for gametangia from the hyphae to be produced and fuse, leading to
karyogamy. The developing diploid zygospores have thick coats that protect
them from desiccation and other hazards. They may remain dormant until
environmental conditions are favorable. When the zygospore germinates, it
undergoes meiosis and produces haploid spores, which will, in turn, grow
into a new organism. This form of sexual reproduction in fungi is called
conjugation (although it differs markedly from conjugation in bacteria and
protists), giving rise to the name “conjugated fungi”.
Zygomycete Life Cycle
Se
Asexual
Germination reproduction Mitosis
Germination:
Mycelia form. If the two mating
types (+ and —) are in close
proximity, extensions called
gametangia form Se Germination
between them.
i ametangia
Sporangium
Mycelia (1n)
(in)
Plasmogamy: ~ Mating type Sexual
Fusion between itt, Re
+ and — mating
types results ina Meiosis and
zygosporangium germination:
with multiple haploid A sporangium grows
nuclei. The Zygosporangium on a short stalk.
zygosporangium Haploid spores are
forms a thick, Ome, = inside.
protective
coat.
EL
The nuclei fuse to
form a zygote with
multiple diploid nuclei.
Zygomycetes have asexual and asexual life
cycles. In the sexual life cycle, plus and minus
mating types conjugate to form a
zygosporangium.
(a) (b)
Sporangia grow at the end of stalks, which appear
as (a) white fuzz seen on this bread mold,
Rhizopus stolonifer. The (b) tips of bread mold are
the spore-containing sporangia. (credit b:
modification of work by "polandeze"/Flickr)
Ascomycota: The Sac Fungi
The majority of known fungi belong to the Phylum Ascomycota, which is
characterized by the formation of an ascus (plural, asci), a sac-like structure
that contains haploid ascospores. Many ascomycetes are of commercial
importance. Some play a beneficial role, such as the yeasts used in baking,
brewing, and wine fermentation, plus truffles and morels, which are held as
gourmet delicacies. Aspergillus oryzae is used in the fermentation of rice to
produce sake. Other ascomycetes parasitize plants and animals, including
humans. For example, fungal pneumonia poses a significant threat to AIDS
patients who have a compromised immune system. Ascomycetes not only
infest and destroy crops directly; they also produce poisonous secondary
metabolites that make crops unfit for consumption. Filamentous
ascomycetes produce hyphae divided by perforated septa, allowing
streaming of cytoplasm from one cell to the other. Conidia and asci, which
are used respectively for asexual and sexual reproductions, are usually
separated from the vegetative hyphae by blocked (non-perforated) septa.
Asexual reproduction is frequent and involves the production of
conidiophores that release haploid conidiospores ({link]). Sexual
reproduction starts with the development of special hyphae from either one
of two types of mating strains ([link]). The “male” strain produces an
antheridium and the “female” strain develops an ascogonium. Next,
cytoplasm of the antheridium and the ascogonium combine in plasmogamy
without nuclear fusion. Special ascogenous hyphae arise, in which pairs of
nuclei migrate: one from the “male” strain and one from the “female”
strain. In each ascus, two or more haploid ascospores fuse their nuclei in
karyogamy. During sexual reproduction, thousands of asci fill a fruiting
body called the ascocarp. The diploid nucleus gives rise to haploid nuclei
by meiosis. These haploid nuclei undergo mitosis and cell divisions to form
haploid ascospores. The ascospores are then released, germinate, and form
hyphae that are disseminated in the environment and start new mycelia
(Link).
Ascomycete Life Cycle
cove
2a
Spores Mitosis
Germination Asexual
eproduction
Plasmogamy ©
and mitosis: &
The ascogonium and aes Conidiophore
antheridium fuse. Mitosis
and cell division result in
the formation of many
dikaryotic hyphae, which Dispersal and
form a fruiting body zz germination
called the ascocarp.
Asci form at the tips
of these hyphae.
(@)
(e)A Ascospores
Mitosis and
cell division:
Eight haploid
Reproduction ascospores
are formed.
SE
Meiosis:
An ascus with four
Ascocarp — haploid nuclei is
Karyogamy: 4 formed.
The nuclei in the ro i
asci fuse to form
a diploid zygote.
The lifecycle of an ascomycete is characterized
by the production of asci during the sexual
phase. The haploid phase is the predominant
phase of the life cycle.
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Ascospores
— ~ —
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The bright field light
micrograph shows
ascospores being released
from asci in the fungus
Talaromyces flavus var.
flavus. (credit:
modification of work by
Dr. Lucille Georg, CDC;
scale-bar data from Matt
Russell)
Basidiomycota: The Club Fungi
The fungi in the Phylum Basidiomycota are easily recognizable under a
light microscope by their club-shaped fruiting bodies called basidia
(singular, basidium), which are the swollen terminal cell of a hypha. This
reproductive organ is the basidiocarp, that contains basidia, and the familiar
mushroom, commonly seen in fields after rain, on the supermarket shelves,
or growing on your lawn ([link]). These mushroom-producing
basidiomyces are sometimes referred to as “gill fungi” because of the
presence of gill-like structures on the underside of the cap. The “gills” are
actually compacted hyphae on which the basidia are borne. This group also
includes shelf fungus, which cling to the bark of trees like small shelves. In
addition, the basidiomycota includes smuts and rusts, which are important
plant pathogens; toadstools, and shelf fungi stacked on tree trunks. Most
edible fungi belong to the Phylum Basidiomycota; however, some
basidiomycetes produce deadly toxins. For example, Cryptococcus
neoformans causes severe respiratory illness.
The fruiting bodies of a
basidiomycete form a ring ina
meadow, commonly called
“fairy ring.” The best-known
fairy ring fungus has the
scientific name Marasmius
oreades. The body of this
fungus, its mycelium, is
underground and grows
outward in a circle. As it grows,
the mycelium depletes the soil
of nitrogen, causing the mycelia
to grow away from the center
and leading to the “fairy ring”
of fruiting bodies where there is
adequate soil nitrogen. (Credit:
"Cropcircles"/Wikipedia
Commons)]|
The lifecycle of basidiomycetes includes alternation of generations ((link]).
Spores are generally produced through sexual reproduction, rather than
asexual reproduction. The club-shaped basidium carries spores called
basidiospores. In the basidium, nuclei of two different mating strains fuse
(karyogamy), giving rise to a diploid zygote that then undergoes meiosis.
The haploid nuclei migrate into basidiospores, which germinate and
generate monokaryotic hyphae. The mycelium that results is called a
primary mycelium. Mycelia of different mating strains can combine and
produce a secondary mycelium that contains haploid nuclei of two different
mating strains. This is the dikaryotic stage of the basidiomyces lifecyle and
and it is the dominant stage. Eventually, the secondary mycelium generates
a basidiocarp, which is a fruiting body that protrudes from the ground—
this is what we think of as a mushroom. The basidiocarp bears the
developing basidia on the gills under its cap.
Basidiomycete Life Cycle
Germination: Basidiospores (n)
Mycelia form. There are @) © @
two mating types (+ and -).
One)
Dispersal and
germination
Plasmogamy:
Fusion between Cell division:
+ and — mating Four
types results in basidiospores
formation of a Sexual | ‘are formed
dikaryotic Reproduction
mycelium. Basidium with
four nuclei
(1n)
Meiosis:
Four haploid nuclei
are formed in the
basidium.
Mitosis:
Under the right ‘O) Zygote
environmental (2n)
conditions, a
basidiocarp forms. Gills
of the basidiocarp contain
cells called basidia. Karyogamy:
aa Basidia form
Basidia diploid nuclei.
Basidiocarp
The lifecycle of a basidiomycete
alternates generation with a prolonged
stage in which two nuclei (dikaryon)
are present in the hyphae.
Deuteromycota:
Those fungi that do not display a sexual phase and only reproduce by
mitospores are classified in the form phylum Deuteromycota.
Deuteromycota is a polyphyletic group where many species are more
closely related to organisms in other phyla than to each other; hence it
cannot be called a true phylum and must, instead, be given the name form
phylum. Since they do not possess the sexual structures that are used to
classify other fungi, they are less well described in comparison to other
divisions. Most members live on land, with a few aquatic exceptions. They
form visible mycelia with a fuzzy appearance and are commonly known as
mold. Molecular analysis shows that the closest group to the
deuteromycetes is the ascomycetes. In fact, some species, such as
Aspergillus, which were once classified as imperfect fungi, are now
classified as ascomycetes.
Reproduction of Deuteromycota is strictly asexual and occurs mostly by
production of asexual conidiospores ({link]). Some hyphae may recombine
and form heterokaryotic hyphae. Genetic recombination is known to take
place between the different nuclei.
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S f
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a
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/ eo
Aspergillus niger is an
imperfect fungus commonly
found as a food contaminant.
The spherical structure in this
light micrograph is a
conidiophore. (credit:
modification of work by Dr.
Lucille Georg, CDC; scale-bar
data from Matt Russell)
The Deuteromycetes have a large impact on everyday human life. The food
industry relies on them for ripening some cheeses. The blue veins in
Roquefort cheese and the white crust on Camembert are the result of fungal
growth. The antibiotic penicillin was originally discovered on an overgrown
Petri plate, on which a colony of Penicillium fungi killed the bacterial
growth surrounding it. Many imperfect fungi cause serious diseases, either
directly as parasites (which infect both plants and humans), or as producers
of potent toxic compounds, as seen in the aflatoxins released by fungi of the
genus Aspergillus.
Glomeromycota: The mitosporic fungi
The Glomeromycota is a newly established phylum which comprises about
230 species that all live in close association with the roots of trees. Fossil
records indicate that trees and their root symbionts share a long
evolutionary history. It appears that all members of this family form
arbuscular mycorrhizae: the hyphae interact with the root cells forming a
mutually beneficial association where the plants supply the carbon source
and energy in the form of carbohydrates to the fungus, and the fungus
supplies essential minerals from the soil to the plant.
The glomeromycetes do not reproduce sexually and do not survive without
the presence of plant roots. Although they have coenocytic hyphae like the
zygomycetes, they do not form zygospores. DNA analysis shows that all
glomeromycetes probably descended from a common ancestor, making
them a monophyletic lineage.
Pathogenic Fungi
Many fungi have negative impacts on other species, including humans and
the organisms they depend on for food. Fungi may be parasites, pathogens,
and, in a very few cases, predators.
Plant Parasites and Pathogens
The production of enough good-quality crops is essential to our existence.
Plant diseases have ruined crops, bringing widespread famine. Most plant
pathogens are fungi that cause tissue decay and eventual death of the host
({link]). In addition to destroying plant tissue directly, some plant pathogens
spoil crops by producing potent toxins. Fungi are also responsible for food
spoilage and the rotting of stored crops. For example, the fungus Claviceps
purpurea causes ergot, a disease of cereal crops (especially of rye).
Although the fungus reduces the yield of cereals, the effects of the ergot’s
alkaloid toxins on humans and animals are of much greater significance: In
animals, the disease is referred to as ergotism. The most common signs and
symptoms are convulsions, hallucination, gangrene, and loss of milk in
cattle. The active ingredient of ergot is lysergic acid, which is a precursor of
the drug LSD. Smuts, rusts, and powdery or downy mildew are other
examples of common fungal pathogens that affect crops.
Some fungal pathogens include (a) green mold on
grapefruit, (b) fungus on grapes, (c) powdery mildew
on a zinnia, and (d) stem rust on a sheaf of barley.
Notice the brownish color of the fungus in (b) Botrytis
cinerea, also referred to as the “noble rot,” which
grows on grapes and other fruit. Controlled infection
of grapes by Botrytis is used to produce strong and
much-prized dessert wines. (credit a: modification of
work by Scott Bauer, USDA ARS; credit b:
modification of work by Stephen Ausmus, USDA
ARS; credit c: modification of work by David
Marshall, USDA ARS; credit d: modification of work
by Joseph Smilanick, USDA ARS)
Aflatoxins are toxic and carcinogenic compounds released by fungi of the
genus Aspergillus. Periodically, harvests of nuts and grains are tainted by
aflatoxins, leading to massive recall of produce, sometimes ruining
producers, and causing food shortages in developing countries.
Animal and Human Parasites and Pathogens
Fungi can affect animals, including humans, in several ways. Fungi attack
animals directly by colonizing and destroying tissues. Humans and other
animals can be poisoned by eating toxic mushrooms or foods contaminated
by fungi. In addition, individuals who display hypersensitivity to molds and
spores develop strong and dangerous allergic reactions. Fungal infections
are generally very difficult to treat because, unlike bacteria, fungi are
eukaryotes. Antibiotics only target prokaryotic cells, whereas compounds
that kill fungi also adversely affect the eukaryotic animal host.
Many fungal infections (mycoses) are superficial and termed cutaneous
(meaning “skin”) mycoses. They are usually visible on the skin of the
animal. Fungi that cause the superficial mycoses of the epidermis, hair, and
nails rarely spread to the underlying tissue ({link]). These fungi are often
misnamed “dermatophytes” from the Greek dermis skin and phyte plant, but
they are not plants. Dermatophytes are also called “ringworms” because of
the red ring that they cause on skin (although the ring is caused by fungi,
not a worm). These fungi secrete extracellular enzymes that break down
keratin (a protein found in hair, skin, and nails), causing a number of
conditions such as athlete’s foot, jock itch, and other cutaneous fungal
infections. These conditions are usually treated with over-the-counter
topical creams and powders, and are easily cleared. More persistent,
superficial mycoses may require prescription oral medications.
“sporangia Sara 2 (A, NNSLN
ae ee a AN!
So <5, 4 PE
Pome <2 fo + Hyphae’* = ) Saha. >
(b) (c)
(a) Ringworm presents as a red ring on the skin. (b)
Trichophyton violaceum is a fungus that causes
superficial mycoses on the scalp. (c) Histoplasma
capsulatum, seen in this X-ray as speckling of light
areas in the lung, is a species of Ascomycota that
infects airways and causes symptoms similar to the
flu. (credit a, b: modification of work by Dr. Lucille K.
Georg, CDC; credit c: modification of work by M
Renz, CDC; scale-bar data from Matt Russell)
Systemic mycoses spread to internal organs, most commonly entering the
body through the respiratory system. For example, coccidioidomycosis
(valley fever) is commonly found in the southwestern United States, where
the fungus resides in the dust. Once inhaled, the spores develop in the lungs
and cause signs and symptoms similar to those of tuberculosis.
Histoplasmosis ({link]c) is caused by the dimorphic fungus Histoplasma
capsulatum; it causes pulmonary infections and, in rare cases, swelling of
the membranes of the brain and spinal cord. Treatment of many fungal
diseases requires the use of antifungal medications that have serious side
effects.
Opportunistic mycoses are fungal infections that are either common in all
environments or part of the normal biota. They affect mainly individuals
who have a compromised immune system. Patients in the late stages of
AIDS suffer from opportunistic mycoses, such as Pneumocystis, which can
be life threatening. The yeast Candida spp., which is a common member of
the natural biota, can grow unchecked if the pH, the immune defenses, or
the normal population of bacteria is altered, causing yeast infections of the
vagina or mouth (oral thrush).
Fungi may even take on a predatory lifestyle. In soil environments that are
poor in nitrogen, some fungi resort to predation of nematodes (small
roundworms). Species of Arthrobotrys fungi have a number of mechanisms
to trap nematodes. For example, they have constricting rings within their
network of hyphae. The rings swell when the nematode touches it and
closes around the body of the nematode, thus trapping it. The fungus
extends specialized hyphae that can penetrate the body of the worm and
slowly digest the hapless prey.
Beneficial Fungi
Fungi play a crucial role in the balance of ecosystems. They colonize most
habitats on Earth, preferring dark, moist conditions. They can thrive in
seemingly hostile environments, such as the tundra, thanks to a most
successful symbiosis with photosynthetic organisms, like lichens. Fungi are
not obvious in the way that large animals or tall trees are. Yet, like bacteria,
they are major decomposers of nature. With their versatile metabolism,
fungi break down organic matter that is insoluble and would not be recycled
otherwise.
Importance to Ecosystems
Food webs would be incomplete without organisms that decompose organic
matter and fungi are key participants in this process. Decomposition allows
for cycling of nutrients such as carbon, nitrogen, and phosphorus back into
the environment so they are available to living things, rather than being
trapped in dead organisms. Fungi are particularly important because they
have evolved enzymes to break down cellulose and lignin, components of
plant cell walls that few other organisms are able to digest, releasing their
carbon content.
Fungi are also involved in ecologically important coevolved symbioses,
both mutually beneficial and pathogenic with organisms from the other
kingdoms. Mycorrhiza, a term combining the Greek roots myco meaning
fungus and rhizo meaning root, refers to the association between vascular
plant roots and their symbiotic fungi. Somewhere between 80—90 percent of
all plant species have mycorrhizal partners. In a mycorrhizal association,
the fungal mycelia use their extensive network of hyphae and large surface
area in contact with the soil to channel water and minerals from the soil into
the plant. In exchange, the plant supplies the products of photosynthesis to
fuel the metabolism of the fungus. Ectomycorrhizae (“outside” mycorrhiza)
depend on fungi enveloping the roots in a sheath (called a mantle) and a net
of hyphae that extends into the roots between cells. In a second type, the
Glomeromycota fungi form arbuscular mycorrhiza. In these mycorrhiza, the
fungi form arbuscles, a specialized highly branched hypha, which penetrate
root cells and are the sites of the metabolic exchanges between the fungus
and the host plant. Orchids rely on a third type of mycorrhiza. Orchids form
small seeds without much storage to sustain germination and growth. Their
seeds will not germinate without a mycorrhizal partner (usually
Basidiomycota). After nutrients in the seed are depleted, fungal symbionts
support the growth of the orchid by providing necessary carbohydrates and
minerals. Some orchids continue to be mycorrhizal throughout their
lifecycle.
Lichens blanket many rocks and tree bark, displaying a range of colors and
textures. Lichens are important pioneer organisms that colonize rock
surfaces in otherwise lifeless environments such as are created by glacial
recession. The lichen is able to leach nutrients from the rocks and break
them down in the first step to creating soil. Lichens are also present in
mature habitats on rock surfaces or the trunks of trees. They are an
important food source for caribou. Lichens are not a single organism, but
rather a fungus (usually an Ascomycota or Basidiomycota species) living in
close contact with a photosynthetic organism (an alga or cyanobacterium).
The body of a lichen, referred to as a thallus, is formed of hyphae wrapped
around the green partner. The photosynthetic organism provides carbon and
energy in the form of carbohydrates and receives protection from the
elements by the thallus of the fungal partner. Some cyanobacteria fix
nitrogen from the atmosphere, contributing nitrogenous compounds to the
association. In return, the fungus supplies minerals and protection from
dryness and excessive light by encasing the algae in its mycelium. The
fungus also attaches the symbiotic organism to the substrate.
Fungi have evolved mutualistic associations with numerous arthropods. The
association between species of Basidiomycota and scale insects is one
example. The fungal mycelium covers and protects the insect colonies. The
scale insects foster a flow of nutrients from the parasitized plant to the
fungus. In a second example, leaf-cutting ants of Central and South
America literally farm fungi. They cut disks of leaves from plants and pile
them up in gardens. Fungi are cultivated in these gardens, digesting the
cellulose that the ants cannot break down. Once smaller sugar molecules are
produced and consumed by the fungi, they in turn become a meal for the
ants. The insects also patrol their garden, preying on competing fungi. Both
ants and fungi benefit from the association. The fungus receives a steady
supply of leaves and freedom from competition, while the ants feed on the
fungi they cultivate.
Importance to Humans
Although we often think of fungi as organisms that cause diseases and rot
food, fungi are important to human life on many levels. As we have seen,
they influence the well-being of human populations on a large scale because
they help nutrients cycle in ecosystems. They have other ecosystem roles as
well. For example, as animal pathogens, fungi help to control the
population of damaging pests. These fungi are very specific to the insects
they attack and do not infect other animals or plants. The potential to use
fungi as microbial insecticides is being investigated, with several species
already on the market. For example, the fungus Beauveria bassiana is a
pesticide that is currently being tested as a possible biological control for
the recent spread of emerald ash borer. It has been released in Michigan,
Illinois, Indiana, Ohio, West Virginia, and Maryland.
The mycorrhizal relationship between fungi and plant roots is essential for
the productivity of farmland. Without the fungal partner in the root systems,
80-90% of trees and grasses would not survive. Mycorrhizal fungal
inoculants are available as soil amendments from gardening supply stores
and promoted by supporters of organic agriculture.
We also eat some types of fungi. Mushrooms figure prominently in the
human diet. Morels, shiitake mushrooms, chanterelles, and truffles are
considered delicacies ({link]). The humble meadow mushroom, Agaricus
campestris, appears in many dishes. Molds of the genus Penicillium ripen
many cheeses. They originate in the natural environment such as the caves
of Roquefort, France, where wheels of sheep milk cheese are stacked to
capture the molds responsible for the blue veins and pungent taste of the
cheese.
The morel mushroom is
an ascomycete that is
much appreciated for its
delicate taste. (credit:
Jason Hollinger)
Fermentation—of grains to produce beer, and of fruits to produce wine—is
an ancient art that humans in most cultures have practiced for millennia.
Wild yeasts are acquired from the environment and used to ferment sugars
into CO, and ethyl alcohol under anaerobic conditions. It is now possible to
purchase isolated strains of wild yeasts from different wine-making regions.
Pasteur was instrumental in developing a reliable strain of brewer’s yeast,
Saccharomyces cerevisiae, for the French brewing industry in the late
1850s. It was one of the first examples of biotechnology patenting. Yeast is
also used to make breads that rise. The carbon dioxide they produce is
responsible for the bubbles produced in the dough that become the air
pockets of the baked bread.
Many secondary metabolites of fungi are of great commercial importance.
Antibiotics are naturally produced by fungi to kill or inhibit the growth of
bacteria, and limit competition in the natural environment. Valuable drugs
isolated from fungi include the immunosuppressant drug cyclosporine
(which reduces the risk of rejection after organ transplant), the precursors of
steroid hormones, and ergot alkaloids used to stop bleeding. In addition, as
easily cultured eukaryotic organisms, some fungi are important model
research organisms including the red bread mold Neurospora crassa and the
yeast, S. cerevisiae.
Lichens, Protists and Green Algae
Introduction
" A process which led from the amoeba to man appeared to the philosophers to be obviously a progress—
though whether the amoeba would agree with this opinion is not known." Bertrand Russell, from "Current
Tendencies", delivered as the first of a series of Lowell Lectures in Boston (Mar 1914).
Lichens
Lichens display a range of colors and textures ({link]) and can survive in the most unusual and hostile
habitats. They cover rocks, gravestones, tree bark, and the ground in the tundra where plant roots cannot
penetrate. Lichens can survive extended periods of drought, when they become completely desiccated,
and then rapidly become active once water is available again.
Lichens have many forms. They may be (a) crust-like, (b) hair-like, or (c) leaf-like. (credit a:
modification of work by Jo Naylor; credit b: modification of work by "djpmapleferryman"/Flickr;
credit c: modification of work by Cory Zanker)
Lichens are an example of a mutualism, in which a fungus (usually a member of the Ascomycota or
Basidiomycota phyla) lives in close contact with a photosynthetic organism (a eukaryotic alga or a
prokaryotic cyanobacterium) ([link]). Generally, neither the fungus nor the photosynthetic organism can
survive alone outside of the symbiotic relationship. The body of a lichen, referred to as a thallus, is
formed of hyphae wrapped around the photosynthetic partner. The photosynthetic organism provides
carbon and energy in the form of carbohydrates. Some cyanobacteria fix nitrogen from the atmosphere,
contributing nitrogenous compounds to the association. In return, the fungus supplies minerals and
protection from dryness and excessive light by encasing the algae in its mycelium. The fungus also
attaches the symbiotic organism to the substrate.
o
This cross-section of a lichen
thallus shows the (a) upper
cortex of fungal hyphae, which
provides protection; the (b)
algal zone where photosynthesis
occurs, the (c) medulla of
fungal hyphae, and the (d)
lower cortex, which also
provides protection and may
have (e) rhizines to anchor the
thallus to the substrate.
Lichens grow very slowly, expanding a few millimeters per year. Both the fungus and the alga participate
in the formation of dispersal units for reproduction. Lichens produce soredia, clusters of algal cells
surrounded by mycelia. Soredia are dispersed by wind and water and form new lichens.
Lichens are extremely sensitive to air pollution, especially to abnormal levels of nitrogen and sulfur. The
U.S. Forest Service and National Park Service can monitor air quality by measuring the relative
abundance and health of the lichen population in an area. Lichens fulfill many ecological roles. Lichens
are often early colonizers of bare rock. Caribou and reindeer eat lichens, and they provide cover for small
invertebrates that hide in the mycelium. In the production of textiles, weavers used lichens to dye wool
for many centuries until the advent of synthetic dyes.
Protists
Amoebae are just one of the creatures that are lumped into the Kingdom Protista, and amoebae and
philosophers do share a common ancestor, as Russell points out. In the span of the last several decades,
the Kingdom Protista has been disassembled and rearranged, as DNA sequence analyses have revealed
new genetic (and therefore evolutionary) relationships among these eukaryotes. Moreover, protists species
that exhibit similar morphological features may not be closely related, but may have evolved analogous
structures because of similar selective pressures — rather than because of recent common ancestry. This
phenomenon, called convergent evolution, is one reason why protist classification is so challenging. The
emerging classification scheme groups the entire domain Eukarya into six “supergroups” that contain all
of the protists as well as animals, plants, and fungi that evolved from a common ancestor ([link]). The
supergroups are hypothesized to be monophyletic, meaning that all organisms within each supergroup are
hypothesized to have evolved from a single common ancestor, and thus all members are more closely
related to each other than to organisms outside that group. There is still evidence lacking for the
monophyly of some groups.
Alveolates
Stramenopiles
Common
eukaryotic
ancestor
Red algae
Chlorophytes
(green algae)
Charophytes
(green algae)
Land plants
Slime molds
Gymnamoebas
Entamoebas
This diagram shows a proposed classification of the
domain Eukara. Currently, the domain Eukarya is
divided into six supergroups. Within each supergroup
are multiple kingdoms. Dotted lines indicate
suggested evolutionary relationships that remain
under debate.
The classification of eukaryotes is still in flux, and the six supergroups may be modified or replaced by a
more appropriate hierarchy as genetic, morphological, and ecological data accumulate. Keep in mind that
the classification scheme presented here is just one of several hypotheses, and the true evolutionary
relationships are still to be determined. For this module, we are focusing on the Archaeplastida which
contain the green algae - the group of organisms most closely related to plants.
Archaeplastida (Red Algae, Green Algae and Plants)
Red algae and green algae are included in the supergroup Archaeplastida. It was from a common ancestor
of these organisms that the land plants evolved, since their closest relatives are found in this group.
Molecular evidence supports that all Archaeplastida are descendents of an endosymbiotic relationship
between a heterotrophic protist and a cyanobacterium. The red and green algae include unicellular,
multicellular, and colonial forms.
Red Algae
Red algae, or rhodophytes, lack flagella and range in size from microscopic unicellular forms to large,
multicellular forms grouped into the informal 'seaweed' category. Most red algae are multicellular. The
red algae life cycle is an alternation of generations (explained in next section). Some species of red algae
contain phycoerythrins, photosynthetic accessory pigments that are red in color and outcompete the green
tint of chlorophyll, making these species appear as varying shades of red. Other species classified as red
algae lack phycoerythrins and are parasites. Red algae are common in tropical waters where they have
been detected at depths of 260 meters. Other red algae exist in terrestrial or freshwater environments.
Red Algae are an economically important food source and additive. Have you ever eaten sushi rolls? If
so, the crispy sheets wrapped around the rice are from the genus Porphyra (Japanese "nori"). The food
stabilizer carrageenan is found in ice cream, yogurt and other food stuffs and is an extract from red algae.
Another extract from red algae commonly used as a thickener and as vegetarian substitute for gelatin is
agar. Agar is also commonly used by microbiologists as a solid substrate to contain culture media in order
to grow bacteria.
Green Algae: Chlorophytes and Charophytes
The most abundant group of algae are the green algae. The green algae exhibit similar features to the land
plants. The cell walls of green algae and land plants are made of cellulose and the chloroplasts of both
groups contain chlorophylls a and b. The hypothesis that this group of protists shared a relatively recent
common ancestor with land plants is well supported. The green algae are subdivided into the chlorophytes
and charophytes. The charophytes are the closest living relatives to land plants and resemble them in
morphology and reproductive strategies. Charophytes are common in wet habitats, and their presence
often signals a healthy ecosystem.
Green algae are as a group of organisms an integral part of a functional ecosystem, and humans have been
using green algae as a food source and as a medicine for a long time. In aquatic environments, green algae
are a Major primary producer and release a substantial amount of oxygen in the system. So a healthy
ecosystem is dependent on a healthy population of green algae. As a economic benefit to humans, green
algae are used a food source (Asakusa Nori) for humans and are used a food thickening agent. Green
algae are used in the agricultural industry as a food source for cattle, and as fertilizer.
The chlorophytes exhibit great diversity of form and function. Chlorophytes primarily inhabit freshwater
and damp soil, and are a common component of plankton. Chlamydomonas is a simple, unicellular
chlorophyte with a pear-shaped morphology and two opposing, anterior flagella that guide this protist
toward light sensed by its eyespot.
Volvox is an example of multicellularity in the Chlorophytes ({link]). Volvox colonies contain 500 to
60,000 cells, each with two flagella, contained within a hollow, spherical matrix composed of a gelatinous
glycoprotein secretion. Volvox moves by rolling in a coordinated fashion. The cells forming the sphere on
the outside do not reproduce while the green cells inside do reproduce, demonstrating division of labor.
Volvox aureus is a green alga in the supergroup Archaeplastida.
This species exists as a colony, consisting of cells immersed in
a gel-like matrix and intertwined with each other via hair-like
cytoplasmic extensions. (credit: Dr. Ralf Wagner)
True multicellular organisms, such as the sea lettuce, Ulva, are represented among the chlorophytes. In
addition, some chlorophytes exist as large, multinucleate, single cells. Species in the genus Caulerpa
exhibit flattened fern-like foliage and can reach lengths of 3 meters ([link]). Caulerpa species undergo
nuclear division, but their cells do not complete cytokinesis, remaining instead as massive and elaborate
single cells.
Caulerpa taxifolia is a chlorophyte
consisting of a single cell
containing potentially thousands
of nuclei. (credit: NOAA)
Charophytes are the closest related green algae to land plants, this conclusion was drawn from studies of
nuclear and chloroplast genes from many different types of plants and algae. In addition to the similarities
listed above, there a some additional structural similarities such as cellulose-synthesizing proteins, the
structure of the flagellated sperm and the gamete producing structures that suggest that land plants arose
from within the charophyta group. This does not mean land plants are descended from living green algae,
but it does allow us to explore the algal ancestor to land plants. For example, the exploration of the Chara
life cycle [link] allows us visualize the similarities between the life cycle of green algae and land plants.
Chara Life Cycle
Haploid (N)
Mitosi,
0
£
aS
. \\ o.
| e ®,
Male \ Female
Spore Beamer. Gametes
of
Diploid (2N) =
Simplified life cycle of Chara. (Work by Robbie Bear, Images credited to "Chara antheridia L" by Jon
Houseman - Jon Houseman and Matthew Ford. Licensed under CC BY-SA 4.0 via Wikimedia
Commons -
http://commons. wikimedia.org/wiki/File:Chara_antheridia_L.jpg#/media/File:Chara_antheridia_L.jp
g "Chara oogonium" by Jon Houseman - Jon Houseman and Matthew Ford. Licensed under CC BY-
SA 4.0 via Wikimedia Commons -
http://commons. wikimedia.org/wiki/File:Chara_oogonium.jpg#/media/File:Chara_oogonium.jpg
"Chara braunii 1" by Show_ryu - Own work. Licensed under CC BY-SA 3.0 via Wikimedia
Commons -
http://commons. wikimedia.org/wiki/File: Chara_braunii_1.JPG#/media/File:Chara_braunii_1.JPG)
Early Plant Life
Introduction
"T observed on most collected stones the imprints of innumerable plant
fragments which were so different from those which are growing in the
Lyonnais, in the nearby provinces, and even in the rest of France, that I felt
like collecting plants in a new world... The number of these leaves, the way
they separated easily, and the great variety of plants whose imprints I saw,
appeared to me just as many volumes of botany representing in the same
quarry the oldest library of the world. " Antoine de Jussieu, French
physician and botanist, 1718
The kingdom Plantae constitutes a large and varied group of organisms,
which have been on the planet for a very long time. There are more than
300,000 species of catalogued plants, including the fossil plants that de
Jussieu references in the epigraph above. Of these, more than 260,000 are
seed plants. Mosses, ferns, conifers, and flowering plants are all members
of the plant kingdom. While there is some disagreement about the
relationships between Chlorophytes, Charophytes, and Plantae, there are
several unique characteristics which these groups share. Only green algae
and plants use chlorophyll a and b plus carotene in a particular ratio. They
share the trait of cellulose-rich cell walls, and there is strong molecular
support for their close relationship.
The ancestors of the green algae became photosynthetic by engulfing a
green, photosynthetic bacterium about 1.65 billion years ago. This captured
bacterium evolved into a chloroplast. That algal line evolved into the
Charophytes, bryophytes, seedless vascular plants, gymnosperms, and
angiosperms.
Several other groups of eukaryotes have common names that include
‘algae.’ In the latest classification red algae are included in Archaeplastida,
while brown algae and golden algae are in a separate supergroup. In
contrast to the green algae, red, golden, and brown algae all became
photosynthetic by secondary, or even tertiary, endosymbiotic events. In
other words, the cells that evolved into red, brown, or golden algae all
engulfed cells that had already engulfed a photosynthetic bacterium. These
algae are also photosynthetic autotrophs, but they did not diversify to the
same extent as the Charophytes, nor did they colonize land.
Plant Adaptations to Life on Land
In order for plants to invade land, they had to contend with several
challenges in the terrestrial environment. Water has been described as “the
stuff of life.” The cell’s interior is a watery soup: in this medium, most
small molecules can dissolve and diffuse rapidly, and the majority of the
chemical reactions of metabolism take place. The first challenge,
Desiccation, or drying out, is a constant danger for an organism exposed to
air. Even when parts of a plant are close to a source of water, the aerial
structures are likely to dry out. Second, Water also provides buoyancy to
organisms. On land, plants need to develop structural support in a medium
that does not give the same support as water. The organism is also subject to
bombardment by mutagenic radiation, because air does not filter out
ultraviolet rays of sunlight like water does. Additionally, the male gametes
must reach the female gametes using new strategies, because swimming is
no longer possible. Lastly, both gametes and zygotes must be protected
from desiccation. The successful land plants developed strategies to deal
with all of these challenges. Not all adaptations appeared at once. Some
species never moved very far from the aquatic environment, whereas others
went on to conquer the driest environments on Earth.
To balance these survival challenges, life on land offers several advantages.
First, sunlight is abundant. Water acts as a filter, altering the spectral quality
of light absorbed by the photosynthetic pigment chlorophyll. Second,
carbon dioxide is more readily available in air than in water, since it
diffuses faster in air. Third, land plants evolved before land animals;
therefore, until dry land was colonized by animals, no predators threatened
plant life. This situation changed as animals emerged from the water and
fed on the abundant sources of nutrients in the established flora. In turn,
plants developed strategies to deter predation: from spines and thorns to
toxic chemicals.
Early land plants, like the early land animals, did not live very far from an
abundant source of water and developed survival strategies to combat
dryness. One of these strategies is called tolerance. Many mosses, for
example, can dry out to a brown and brittle mat, but as soon as rain or a
flood makes water available, mosses will absorb it and are restored to their
healthy green appearance. Another strategy is to colonize environments
with high humidity, where droughts are uncommon. Ferns, which are
considered an early lineage of plants, thrive in damp and cool places such
as the understory of temperate forests. Later, plants moved away from moist
or aquatic environments using resistance to desiccation, rather than
tolerance. These plants, like cacti, minimize the loss of water to such an
extent they can survive in extremely dry environments.
The most successful adaptation was the development of new structures that
gave plants the advantage when colonizing new and dry environments. Four
major adaptations are found in all terrestrial plants: the alternation of
generations, a sporangium in which the spores are formed, a gametangium
that produces haploid cells, and apical meristem tissue in roots and shoots.
The evolution of a waxy cuticle and a cell wall with lignin also contributed
to the success of land plants. These adaptations are noticeably lacking in the
closely related green algae.
Alternation of Generations
Alternation of generations describes a life cycle in which an organism has
both haploid and diploid multicellular stages ([link]).
Generalized Plant Life Cycle
Alternation of generations between the 1N gametophyte and 2N
sporophyte is shown. Work by Eva Horne and Robert A. Bear
Most plants exhibit alternation of generations, wherein the haploid
multicellular form, known as a gametophyte, is followed in the
development sequence by a multicellular diploid organism: the sporophyte.
The gametophyte gives rise to the gametes (reproductive cells) by mitosis.
This can be the most obvious phase of the life cycle of the plant, as in the
mosses, or it can occur in a microscopic structure, such as a pollen grain, in
the higher plants (a common collective term for the vascular plants). The
sporophyte stage is barely noticeable in lower plants (the collective term for
the plant groups of mosses, liverworts, and hornworts). Towering trees are
the diploid, sporophyte phase in the lifecycles of plants such as sequoias
and pines.
Protection of the embryo is a major requirement for land plants. Embryos
have a high surface area to volume ratio, and thus are vulnerable to
desiccation and other environmental hazards. In both seedless and seed
plants, the female gametophyte provides protection and nutrients to the
embryo as it develops into the new generation of sporophyte. This
distinguishing feature of land plants gave the group its alternate name of
embryophytes.
Sporangia in Seedless Plants
The sporophyte of seedless plants is diploid and results from syngamy
(fusion) of two gametes. The sporophyte bears the sporangia (singular,
sporangium): organs that first appeared in the land plants. The term
“sporangia” literally means “spore in a vessel,” as it is a reproductive sac
that contains spores [link]. Inside the multicellular sporangia, the diploid
sporocytes, or mother cells, produce haploid spores by meiosis, where the
2N chromosome number is reduced to 1N (note that many plant
sporophytes are polyploid: for example, durum wheat is tetraploid (4N),
bread wheat is hexaploid (6N), and some ferns are 1000-ploid). The spores
are later released by the sporangia and disperse in the environment. Two
different types of spores are produced in land plants, resulting in the
separation of sexes at different points in the lifecycle. Seedless non-
vascular plants produce only one kind of spore and are called
homosporous. The gametophyte phase is dominant in these plants. After
germinating from a spore, the resulting gametophyte produces both male
and female gametangia, usually on the same individual. In contrast,
heterosporous plants produce two morphologically different types of
spores. The male spores are called microspores, because of their smaller
size, and develop into the male gametophyte; the comparatively larger
megaspores develop into the female gametophyte. Heterospory is observed
in a few seedless vascular plants and in all seed plants.
Spore-producing sacs called
sporangia grow at the ends of
long, thin stalks in this photo of
the moss Esporangios bryum.
(credit: Javier Martin)
When the haploid spore germinates in a hospitable environment, it grows
into a multicellular gametophyte by mitosis. The gametophyte supports the
zygote formed from the fusion of gametes and the resulting young
sporophyte (vegetative form). The cycle then begins anew.
The spores of seedless plants are surrounded by thick cell walls containing
a tough polymer known as sporopollenin. This complex substance is
characterized by long chains of organic molecules related to fatty acids and
carotenoids: hence the yellow color of most pollen. Sporopollenin is
unusually resistant to chemical and biological degradation. In seed plants,
which use pollen (the microspore) to transfer the male sperm to the female
egg, the toughness of sporopollenin explains the existence of well-
preserved pollen fossils. Sporopollenin was once thought to be an
innovation of land plants; however, the green algae Coleochaetes forms
spores that contain sporopollenin.
Gametangia in Seedless Plants
Gametangia (singular, gametangium) are structures observed on
multicellular haploid gametophytes. In the gametangia, precursor cells give
rise to gametes by mitosis. The male gametangium (antheridium) releases
sperm. Many seedless plants produce sperm equipped with flagella that
enable them to swim in a moist environment to the archegonia: the female
gametangium. The embryo develops inside an archegonium into a
multicellular sporophyte. Gametangia are prominent in seedless plants, but
are very rarely found in seed plants.
Apical Meristems
Shoots and roots of plants increase in length through rapid cell division in a
tissue called the apical meristem, which is a small zone of cells found at the
shoot tip or root tip ([link]). The apical meristem is made of
undifferentiated cells that continue to proliferate throughout the life of the
plant. Meristematic cells give rise to all the specialized tissues of the
organism. Elongation of the shoots and roots allows a plant to access
additional space and resources: light in the case of the shoot, and water and
minerals in the case of roots. A separate meristem, called the lateral
meristem, produces cells that increase the diameter of tree trunks.
Apical meristem
Root cap
Addition of new cells in a
root occurs at the apical
meristem. Subsequent
enlargement of these cells
causes the organ to grow and
elongate. The root cap
protects the fragile apical
meristem as the root tip is
pushed through the soil by
cell elongation.
Additional Land Plant Adaptations
As plants adapted to dry land and became independent from the constant
presence of water in damp habitats, new organs and structures made their
appearance. Early land plants did not grow more than a few inches off the
ground, competing for light on these low mats. By developing a shoot and
growing taller, individual plants captured more light. Because air offers
substantially less support than water, land plants incorporated more rigid
molecules in their stems (and later, tree trunks). In small organisms such as
single-celled algae, simple diffusion suffices to distribute water and
nutrients throughout the organism. However, for plants to evolve larger
forms, the evolution of vascular tissue for the distribution of water and
solutes was a prerequisite. The vascular system contains xylem and phloem
tissues. Xylem conducts water and minerals absorbed from the soil up to
the shoot, while phloem transports food derived from photosynthesis
throughout the entire plant. A root system evolved to take up water and
minerals from the soil, and to anchor the increasingly taller shoot in the soil.
In land plants, a waxy, waterproof cover called a cuticle protects the leaves
and stems from desiccation. However, the cuticle also prevents intake of
carbon dioxide needed for the synthesis of carbohydrates through
photosynthesis. To overcome this, stomata or pores that open and close to
regulate traffic of gases and water vapor evolved in plants as they moved
away from moist environments into drier habitats.
Lignin is a complex polymer predominantly found in the cell walls of
xylem, it forms crosslinks between the cellulose molecules. Since lignin is
interwoven into the cell walls, it adds strength to the cell wall and therefore
the entire plant. In addition, lignin is a hydrophobic compound that allows
for the more efficient transport of water in the vascular tissue.
Water filters ultraviolet-B (UVB) light, which is harmful to all organisms,
especially those that must absorb light to survive. This filtering does not
occur for land plants. This presented an additional challenge to land
colonization, which was met by the evolution of biosynthetic pathways for
the synthesis of protective flavonoids and other compounds: pigments that
absorb UV wavelengths of light and protect the aerial parts of plants from
photodynamic damage.
Plants cannot avoid being eaten by animals. Instead, they synthesize a large
range of poisonous secondary metabolites: complex organic molecules such
as alkaloids, whose noxious smells and unpleasant taste deter animals.
These toxic compounds can also cause severe diseases and even death, thus
discouraging predation. Humans have used many of these compounds for
centuries as drugs, medications, or spices. In contrast, as plants co-evolved
with animals, the development of sweet and nutritious metabolites lured
animals into providing valuable assistance in dispersing pollen grains, fruit,
or seeds. Plants have been enlisting animals to be their helpers in this way
for hundreds of millions of years.
Evolution of Land Plants
No discussion of the evolution of plants on land can be undertaken without
a brief review of the timeline of the geological eras. The early era, known
as the Paleozoic, is divided into six periods. It starts with the Cambrian
period, followed by the Ordovician, Silurian, Devonian, Carboniferous, and
Permian. The major event to mark the Ordovician, more than 500 million
years ago, was the colonization of land by the ancestors of modern land
plants. Fossilized cells, cuticles, and spores of early land plants have been
dated as far back as the Ordovician period in the early Paleozoic era. The
oldest-known vascular plants have been identified in deposits from the
Devonian. One of the richest sources of information is the Rhynie chert, a
sedimentary rock deposit found in Rhynie, Scotland ([link]), where
embedded fossils of some of the earliest vascular plants have been
identified.
(b)
This Rhynie chert contains fossilized material from
vascular plants. The area inside figure a contains
bulbous underground stems called corms, and root-
like structures called rhizoids. (credit b: modification
of work by Peter Coxhead based on original image
by “Smith609”/Wikimedia Commons; scale-bar data
from Matt Russell)
Paleobotanists distinguish between extinct species, as fossils, and extant
species, which are still living. The extinct vascular plants, classified as
zosterophylls and trimerophytes, most probably lacked true leaves and roots
and formed low vegetation mats similar in size to modern-day mosses,
although some trimetophytes could reach one meter in height. The later
genus Cooksonia, which flourished during the Silurian, has been
extensively studied from well-preserved examples. Imprints of Cooksonia
show slender branching stems ending in what appear to be sporangia. From
the recovered specimens, it is not possible to establish for certain whether
Cooksonia possessed vascular tissues. Fossils indicate that by the end of the
Devonian period, ferns, horsetails, and seed plants populated the landscape,
giving rising to trees and forests. This luxuriant vegetation helped enrich
the atmosphere in oxygen, making it easier for air-breathing animals to
colonize dry land. Plants also established early symbiotic relationships with
fungi, creating mycorrhizae: a relationship in which the fungal network of
filaments increases the efficiency of the plant root system, and the plants
provide the fungi with byproducts of photosynthesis.
Note:
Career Connection
Paleobotanist
How organisms acquired traits that allow them to colonize new
environments—and how the contemporary ecosystem is shaped—are
fundamental questions of evolution. Paleobotany (the study of extinct
plants) addresses these questions through the analysis of fossilized
specimens retrieved from field studies, reconstituting the morphology of
organisms that disappeared long ago. Paleobotanists trace the evolution of
plants by following the modifications in plant morphology: shedding light
on the connection between existing plants by identifying common
ancestors that display the same traits. This field seeks to find transitional
species that bridge gaps in the path to the development of modern
organisms. Fossils are formed when organisms are trapped in sediments or
environments where their shapes are preserved. Paleobotanists collect
fossil specimens in the field and place them in the context of the geological
sediments and other fossilized organisms surrounding them. The activity
requires great care to preserve the integrity of the delicate fossils and the
layers of rock in which they are found.
One of the most exciting recent developments in paleobotany is the use of
analytical chemistry and molecular biology to study fossils. Preservation of
molecular structures requires an environment free of oxygen, since
oxidation and degradation of material through the activity of
microorganisms depend on its presence. One example of the use of
analytical chemistry and molecular biology is the identification of
oleanane, a compound that deters pests. Up to this point, oleanane
appeared to be unique to flowering plants; however, it has now been
recovered from sediments dating from the Permian, much earlier than the
current dates given for the appearance of the first flowering plants.
Paleobotanists can also study fossil DNA, which can yield a large amount
of information, by analyzing and comparing the DNA sequences of extinct
plants with those of living and related organisms. Through this analysis,
evolutionary relationships can be built for plant lineages.
Paleobotanists must be cautious when drawing conclusions from the
analysis of molecular fossils. Chemical materials of interest degrade
rapidly when exposed to air during their initial isolation, as well as in
further manipulations. There is always a risk of contaminating the
specimens with extraneous material, mostly from microorganisms.
Nevertheless, as technology is refined, the analysis of DNA from fossilized
plants will provide invaluable information on the evolution of plants and
their adaptation to an ever-changing environment.
The Major Divisions of Land Plants
Land plants are classified into two major groups according to the absence or
presence of vascular tissue, as detailed in [link]. Plants that lack vascular
tissue, which is formed of specialized cells for the transport of water and
nutrients, are referred to as non-vascular plants. Liverworts, mosses, and
hornworts are seedless, non-vascular plants that likely appeared early in
land plant evolution. Vascular plants developed a network of cells that
conduct water and solutes. The first vascular plants appeared in the middle
Paleozoic and were probably similar to lycophytes, which include club
mosses (not to be confused with the mosses) and the pterophytes (ferns,
horsetails, and whisk ferns). Lycophytes and pterophytes are referred to as
seedless vascular plants, because they do not produce seeds. The seed
plants, or spermatophytes, form the largest group of all existing plants, and
hence dominate the landscape. Seed plants include Gymnosperms, most
notably conifers (Gymnosperms), which produce “naked seeds,” and the
most successful of all plants, the flowering plants (Angiosperms).
Angiosperms protect their seeds inside chambers at the center of a flower;
the walls of the chamber later develop into a fruit.
Note:
Flowers and Fruits
Angiosperms
Seeds Gnetophytes
Conifers
Vascular Ginkgos Gymnosperms
Tissue Cycads
True ferns
Horsetails Seedless
Whisk ferns Vascular
Land Club mosses
Plants
Mosses
Hornworts Bryophytes
Liverworts
500 400 300 200 100 0
Time (millions of year ago)
This figure shows the major divisions of green plants and when
various adaptations for land life evolved. Work by Robert A. Bear
Bryophytes
Introduction
"It was to Hofmeister, working as a young man, an amateur and enthusiast,
in the early morning hours of summer months, before business, at Leipzig
in the years before 1851, that the vision first appeared of a common type of
Life-Cycle, running through Mosses and Ferns to Gymnosperms and
Flowering Plants, linking the whole series in one scheme of reproduction
and life-history." Arthur Harry Church, 1919. As quoted in E.J.H. Corner,
The Life of Plants (1964)
The commonality of the plant life cycle unites the Plant Kingdom,
indicating that it appeared very early in the evolution of plants. The
Bryophytes are the group of plants that are the closest extant relative of
those early terrestrial plants. The first bryophytes (liverworts) most likely
appeared in the Ordovician period, about 450 million years ago. Because of
the lack of lignin and other resistant structures, the likelihood of bryophytes
forming fossils is rather small. Some spores protected by sporopollenin
have survived and are attributed to early bryophytes. By the Silurian period,
however, vascular plants had spread through the continents. This
compelling fact is used as evidence that non-vascular plants must have
preceded the Silurian period.
More than 25,000 species of bryophytes thrive in mostly damp habitats,
although some live in deserts. They constitute the major flora of
inhospitable environments like the tundra, where their small size and
tolerance to desiccation offer distinct advantages. They generally lack lignin
and do not have actual tracheids (xylem cells specialized for water
conduction). Rather, water and nutrients circulate inside specialized
conducting cells. Although the term non-tracheophyte is more accurate,
bryophytes are commonly called non-vascular plants.
In a bryophyte, all the conspicuous vegetative organs—including the
photosynthetic leaf-like structures, the thallus, stem, and the rhizoid that
anchors the plant to its substrate—belong to the haploid organism or
gametophyte. The sporophyte is barely noticeable. The gametes formed by
bryophytes swim with a flagellum, as do gametes in a few of the vascular
plants. The sporangium—the multicellular sexual reproductive structure—is
present in bryophytes and absent in the majority of algae. The bryophyte
embryo also remains attached to the parent plant, which protects and
nourishes it. This is a characteristic of land plants.
The Bryophyte life cycle follows the pattern of alternation of generations as
shown in [link]. The most familiar structure is the haploid gametophyte,
which germinates from a haploid spore. Cells similar to an apical meristem
actively divide and give rise to the photosynthetic stem and leaf-like
structures. Sperm and egg producing structures form on separate or the
same stems. Sperm swim along the bryophte and unite with the egg inside
the egg-producing structure (archegonium). The zygote, protected by this
structure, divides and grows into a sporophyte, still attached to the
gametophyte. The sporophyte forms spores by meiosis; these disperse and
will form new gametophytes.
Bryophyte Life Cycle
This illustration shows the generalized life cycle of bryophytes. Work
by Eva Horne and Robert A. Bear
The bryophytes are divided into three phyla: the liverworts or
Hepaticophyta, the hornworts or Anthocerotophyta, and the mosses or true
Bryophyta. The organisms in these three phyla share the following
characteristics. Bryophytes lack vascular tissue, lack true leaves, lack seeds,
use spores as a means of dispersal and have the gametophyte generation as
the dominant (conspicuous) part of the life cycle. Even with all these
characteristics in common, molecular and other evidence suggests that they
do not form a single clade (a group that includes one common ancestor and
all of its descendants)
Liverworts
Liverworts (Hepaticophyta) are viewed as the plants most closely related
to the ancestor that moved to land. Liverworts have colonized every
terrestrial habitat on Earth and diversified to more than 7,000 existing
species ({link]). Some gametophytes form lobate green structures, as seen in
[link]. The shape is similar to the lobes of the liver, and hence provides the
origin of the name given to the phylum. Openings that allow the movement
of gases may be observed in liverworts. However, these openings are not
stomata, because they do not actively open and close. The plant takes up
water over its entire surface and has no cuticle to prevent desiccation.
This 1904 drawing shows the
variety of forms of
liverworts.
A liverwort, Lunularia cruciata,
displays its lobate, flat thallus. The
organism in the photograph is in
the gametophyte stage.
The lifecycle of a liverwort starts with the release of haploid spores from
the sporangium that developed on the sporophyte. Spores disseminated by
wind or water germinate into flattened thalli attached to the substrate by
thin, single-celled filaments. Male and female gametangia develop on
separate, individual plants. Once released, male gametes swim with the aid
of their flagella to the female gametangium (the archegonium), and
fertilization ensues. The zygote grows into a small sporophyte still attached
to the parent gametophyte. It will give rise, by meiosis, to the next
generation of spores. Liverwort plants can also reproduce asexually, by the
breaking of branches or the spreading of leaf fragments called gemmae. In
this latter type of reproduction, the gemmae—small, intact, complete pieces
of plant that are produced in a cup on the surface of the thallus are splashed
out of the cup by raindrops. The gemmae then land nearby and develop into
gametophytes.
Hornworts
The hornworts (Anthocerotophyta) have colonized a variety of habitats on
land, although they are never far from a source of moisture. The short, blue-
green gametophyte is the dominant phase of the lifecycle of a hornwort.
The narrow, pipe-like sporophyte is the defining characteristic of the group.
The sporophytes emerge from the parent gametophyte and continue to grow
throughout the life of the plant ([link]).
Hornworts grow a tall and
slender sporophyte. (credit:
modification of work by
Jason Hollinger)
Stomata appear in the hormworts and are abundant on the sporophyte.
Photosynthetic cells in the thallus contain a single chloroplast. Meristem
cells at the base of the plant keep dividing and adding to its height. Many
hornworts establish symbiotic relationships with cyanobacteria that fix
nitrogen from the environment.
The lifecycle of hornworts follows the general pattern of alternation of
generations. The gametophytes grow as flat thalli on the soil with
embedded gametangia. Flagellated sperm swim to the archegonia and
fertilize eggs. The zygote develops into a long and slender sporophyte that
eventually splits open, releasing spores. The haploid spores germinate and
give rise to the next generation of gametophyte.
Mosses
More than 10,000 species of mosses have been catalogued. Their habitats
vary from the tundra, where they are the main vegetation, to the understory
of tropical forests. In the tundra, the mosses’ shallow rhizoids allow them to
fasten to a substrate without penetrating the frozen soil. Mosses slow down
erosion, store moisture and soil nutrients, and provide shelter for small
animals as well as food for larger herbivores, such as the musk ox. Mosses
are very sensitive to air pollution and are used to monitor air quality. They
are also sensitive to copper salts, so these salts are a common ingredient of
compounds marketed to eliminate mosses from lawns.
Mosses form diminutive gametophytes, which are the dominant phase of
the lifecycle. Green, flat structures—resembling true leaves, but lacking
vascular tissue—are attached in a spiral to a central stalk. The plants absorb
water and nutrients directly through these leaf-like structures. Some mosses
have small branches. Some primitive traits of green algae, such as
flagellated sperm, are still present in mosses that are dependent on water for
reproduction. Other features of mosses are clearly adaptations to dry land.
For example, stomata are present on the stems of the sporophyte, and a
primitive vascular system runs up the sporophyte’s stalk. Additionally,
mosses are anchored to the substrate—whether it is soil, rock, or roof tiles
—by multicellular rhizoids. These structures are precursors of roots. They
originate from the base of the gametophyte, but are not the major route for
the absorption of water and minerals. The lack of a true root system
explains why it is so easy to rip moss mats from a tree trunk. The moss
lifecycle follows the pattern of alternation of generations as shown in [link].
Seedless Vascular Plants
Introduction
"We might expect... in the summer of the ‘great year,’ which we are now
considering, that there would be a great predominance of tree-ferns and
plants allied to the palms and arborescent grasses in the isles of the wide
ocean, while the dicotyledenous plants and other forms now most common
in temperate regions would almost disappear from the earth. Then might
these genera of animals return, of which the memorials are preserved in the
ancient rocks of our continents. The huge iguanodon might reappear in the
woods, and the ichthyosaur in the sea, while the pterodactyle might flit
again through umbrageous groves of tree-ferns. Coral reefs might be
prolonged beyond the arctic circle, where the whale and narwal [sic] now
abound. Turtles might deposit their eggs in the sand of the sea beach, where
now the walrus sleeps, and where the seal is drifted on the ice-floe. " Sir
Charles Lyell, Principles of Geology, (1830)
Lyell's book, which greatly influenced scientists in the time of Darwin,
appeared just as science was comprehending the value of the fossil record
in reconstructing the history of life on earth. Fossilized tree-ferns from coal
mines in Britain and North America gave hints of an ancient time of lush
tropical forests in those regions, and how and when those forests
disappeared was a mystery waiting to be solved. The vascular plants,
including ferns and their allies, are the dominant and most conspicuous
group of land plants. More than 260,000 species (including ferns,
gymnosperms and angiosperms) represent more than 90 percent of Earth’s
vegetation. Several evolutionary innovations explain their success and their
ability to spread to all habitats.
A tree-fern in New Zealand
A modern tree-fern in the forests of New
Zealand. This particular species is the Silver
Fern (Cyathea dealbata), the national
symbol of New Zealand, which appears on
the uniforms of the national Rugby Team,
the All Blacks.
Bryophytes may have been successful at the transition from an aquatic
habitat to land, but they are still dependent on water for reproduction, and
absorb moisture and nutrients through the gametophyte surface. The lack of
roots for absorbing water and minerals from the soil, as well as a lack of
reinforced conducting cells, limits bryophytes to small sizes. Although they
may survive in reasonably dry conditions, they cannot reproduce and
expand their habitat range in the absence of water. Vascular plants, on the
other hand, can achieve enormous heights, thus competing successfully for
light. Photosynthetic organs become leaves, and pipe-like cells or vascular
tissues transport water, minerals, and fixed carbon throughout the organism.
In seedless vascular plants, the diploid sporophyte is the dominant phase of
the lifecycle. The gametophyte is now an inconspicuous, but still
independent, organism. Throughout plant evolution, there is an evident
reversal of roles in the dominant phase of the lifecycle. Seedless vascular
plants still depend on water during fertilization, as the sperm must swim on
a layer of moisture to reach the egg. This step in reproduction explains why
ferns and their relatives are more abundant in damp environments.
Characteristics of Seedless Vascular Plants
As the name implies, this group of plants lack seeds and fruit but do have
vascular tissue. The vascular tissue xylem and phloem are used to move
water throughout the plant and there is lignin found in the cell walls for
structural support and for enhanced water transport efficiency. However,
water is still necessary for sperm to swim to the egg and why many ferns
and their relatives are found in damp environments. Lastly, the sporophyte
is the dominant phase of the life cycle with the gametophyte being and
inconspicuous and independent organism.
Vascular Tissue: Xylem and Phloem
The first fossils that show the presence of vascular tissue date to the
Silurian period, about 430 million years ago. The simplest arrangement of
conductive cells shows a pattern of xylem at the center surrounded by
phloem. Xylem is the tissue responsible for the storage and long-distance
transport of water and nutrients, as well as the transfer of water-soluble
growth factors from the organs of synthesis to the target organs. The tissue
consists of conducting cells, known as tracheids, and supportive filler
tissue, called parenchyma. Xylem conductive cells incorporate the
compound lignin into their walls, and are thus described as lignified. Lignin
itself is a complex polymer that is impermeable to water and strengthens
vascular tissue. With their rigid cell walls, the xylem cells provide support
to the plant and allow it to achieve impressive heights. Tall plants have a
selective advantage by being able to reach unfiltered sunlight and disperse
their spores or seeds further away, thus expanding their range. By growing
higher than other plants, tall trees cast their shadow on shorter plants and
limit competition for water and precious nutrients in the soil.
Phloem is the second type of vascular tissue; it transports sugars, proteins,
and other solutes throughout the plant. Phloem cells are divided into sieve
elements (conducting cells) and cells that support the sieve elements.
Together, xylem and phloem tissues form the vascular system of plants.
Roots: Support for the Plant
Roots are not well preserved in the fossil record. Nevertheless, it seems that
roots appeared later in evolution than vascular tissue. The development of
an extensive network of roots represented a significant new feature of
vascular plants. Thin rhizoids attached bryophytes to the substrate, but these
rather flimsy filaments did not provide a strong anchor for the plant; neither
did they absorb substantial amounts of water and nutrients. In contrast,
roots, with their prominent vascular tissue system, transfer water and
minerals from the soil to the rest of the plant. The extensive network of
roots that penetrates deep into the soil to reach sources of water also
stabilizes plants by acting as a ballast or anchor. The majority of roots
establish a mulutalistic relationship with fungi, forming mycorrhizae, which
benefit the plant by greatly increasing the surface area for absorption of
water and soil minerals and nutrients.
Leaves, Sporophylls, and Strobili
A third adaptation marks the seedless vascular plants. Accompanying the
prominence of the sporophyte and the development of vascular tissue, the
evolution of true leaves improved photosynthetic efficiency. Leaves capture
more sunlight with their increased surface area by employing more
chloroplasts to trap light energy and convert it to chemical energy, which is
then used to fix atmospheric carbon dioxide into carbohydrates. The
carbohydrates are exported to the rest of the plant by the conductive cells of
phloem tissue.
The existence of two types of morphology suggests that leaves evolved
independently in several groups of plants. The first type of leaf is the
microphyll, or “little leaf,” which can be dated to 350 million years ago in
the late Silurian. A microphyll is small and has a simple vascular system. A
single unbranched vein—a bundle of vascular tissue made of xylem and
phloem—truns through the center of the leaf. Microphylls may have
originated from the flattening of lateral branches, or from sporangia that
lost their reproductive capabilities. Microphylls are present in the club
mosses and probably preceded the development of megaphylls, or “big
leaves”, which are larger leaves with a pattern of branching veins.
Megaphylls most likely appeared independently several times during the
course of evolution. Their complex networks of veins suggest that several
branches may have combined into a flattened organ, with the gaps between
the branches being filled with photosynthetic tissue.
In addition to photosynthesis, leaves play another role in the lives of plants.
Pine cones, mature fronds of ferns, and flowers are all sporophylls—leaves
that were modified structurally to bear sporangia. Strobili are cone-like
structures that contain sporangia. They are prominent in conifers and are
commonly known as pine cones.
Ferns and Other Seedless Vascular Plants
By the late Devonian period, plants had evolved vascular tissue, well-
defined leaves, and root systems. With these advantages, plants increased in
height and size. During the Carboniferous period, swamp forests of club
mosses and horsetails—some specimens reaching heights of more than 30
m (100 ft)—covered most of the land. These forests gave rise to the
extensive coal deposits that gave the Carboniferous its name. In seedless
vascular plants, the sporophyte became the dominant phase of the lifecycle.
Water is still required for fertilization of seedless vascular plants, and most
favor a moist environment. Modern-day seedless vascular plants include
club mosses, horsetails, ferns, and whisk ferns.
Phylum Lycopodiophyta: Club Mosses
The club mosses, or phylum Lycopodiophyta, are the earliest group of
seedless vascular plants. They dominated the landscape of the
Carboniferous, growing into tall trees and forming large swamp forests.
Today’s club mosses are diminutive, evergreen plants consisting of a stem
(which may be branched) and microphylls ({link]). The phylum
Lycopodiophyta consists of close to 1,200 species, including quillworts
(Isoetales), club mosses (Lycopodiales), and spike mosses (Selaginellales),
which, despite their common names, are not true mosses (bryophytes).
Lycophytes follow the pattern of alternation of generations seen in the
bryophytes, except that the sporophyte is the major stage of the lifecycle.
The gametophytes do not depend on the sporophyte for nutrients. Some
gametophytes develop underground and form mycorrhizal associations with
fungi. In club mosses, the sporophyte gives rise to sporophylls arranged in
strobili, cone-like structures that give the class its name. Lycophytes can be
homosporous or heterosporous.
In the club mosses such as
Lycopodium clavatum,
sporangia are arranged in
clusters called strobili. (credit:
Cory Zanker)
Phylum Monilophyta: Class Equisetopsida (Horsetails)
Horsetails, whisk ferns and ferns belong to the phylum Monilophyta, with
horsetails placed in the Class Equisetopsida. The modern genus Equisetum
contains the only survivors of a large and diverse group of horsetails known
as the Arthrophyta, which produced large trees and entire swamp forests
during the Carboniferous. The plants are usually found in damp
environments and marshes ([link]).
Horsetails thrive in a marsh.
(credit: Myriam Feldman)
The stem of a horsetail is characterized by the presence of joints or nodes,
hence the name Arthrophyta (arthro- = "joint"; -phyta = "plant"). Leaves
and branches come out as whorls from the evenly spaced joints. The needle-
shaped leaves do not contribute greatly to photosynthesis, the majority of
which takes place in the green stem ([link]).
Thin leaves originating at
the joints are noticeable
on the horsetail plant.
Horsetails were once used
as scrubbing brushes and
were nicknamed scouring
brushes. (credit: Myriam
Feldman)
Silica collects in the epidermal cells, contributing to the stiffness of
horsetail plants. Underground stems known as rhizomes anchor the plants to
the ground. Modern-day horsetails are homosporous and an individual
produces both male and female gametes.
Phylum Monilophyta: Class Psilotopsida (Whisk Ferns)
While most ferns form large leaves and branching roots, the whisk ferns,
Class Psilotopsida, lack both roots and leaves. Photosynthesis takes place in
their green stems, and small yellow knobs form at the tip of the branch stem
and contain the sporangia.
The whisk fern Psilotum nudum
has conspicuous green stems
with knob-shaped sporangia.
(credit: Forest & Kim Starr)
Phylum Monilophyta: Class Psilotopsida (Ferns)
Ferns are the most readily recognizable seedless vascular plants and are
considered the most advanced seedless vascular plants because they display
characteristics commonly observed in seed plants. More than 20,000
species of ferns live in environments ranging from tropics to temperate
forests. Although some species survive in dry environments, most ferns are
restricted to moist, shaded places. Ferns made their appearance in the fossil
record during the Devonian period and expanded during the Carboniferous.
The dominant stage of the lifecycle of a fern is the sporophyte, which
consists of large compound leaves called fronds. Fronds fulfill a double
role; they are photosynthetic organs that also carry reproductive organs. The
stem may be buried underground as a rhizome, from which adventitious
roots grow to absorb water and nutrients from the soil; or, they may grow
above ground as a trunk in tree ferns ([link]). Adventitious organs are those
that grow in unusual places, such as roots growing from the side of a stem.
Some specimens of this short
tree-fern species can grow very
tall. (credit: Adrian Pingstone)
The tip of a developing fern frond is rolled into a crozier, or fiddlehead
({link]Ja and [link]b). Fiddleheads unroll as the frond develops.
Croziers, or fiddleheads, are the tips of
fern fronds. (credit a: modification of
work by Cory Zanker; credit b:
modification of work by Myriam
Feldman)
The lifecycle of a fern is depicted in [link].
Fern Life Cycle
This life cycle of a fern shows alternation of generations with a
dominant sporophyte stage. Work by Eva Horne and Robert A. Bear
Most ferns produce a single type of spore and are therefore homosporous.
The diploid sporophyte is the most conspicuous stage of the lifecycle. On
the underside of its mature fronds, sori (singular, sorus) form as small
clusters where sporangia develop ([link]).
Sori appear as small bumps on the
underside of a fern frond. (credit:
Myriam Feldman)
Inside the sori, spores are produced by meiosis and released into the air.
Those that land on a suitable substrate germinate and form a heart-shaped
gametophyte, which is attached to the ground by thin filamentous rhizoids
([link]).
Sporophyte
ee Gametophyte hm
Shown here are a young
sporophyte (upper part of image)
and a heart-shaped gametophyte
(bottom part of image). (credit:
modification of work by
"VImastra"/Wikimedia Commons)
The inconspicuous gametophyte harbors both sex gametangia. Flagellated
sperm released from the antheridium swim on a wet surface to the
archegonium, where the egg is fertilized. The newly formed zygote grows
into the next generation sporophyte.
The Importance of Bryophytes and Seedless Vascular Plants
Mosses and liverworts are often the first macroscopic organisms to colonize
an area, both in a primary succession—where bare land is settled for the
first time by living organisms—or in a secondary succession, where soil
remains intact after a catastrophic event wipes out many existing species.
Their spores are carried by the wind, birds, or insects. Once mosses and
liverworts are established, they provide food and shelter for other species.
In a hostile environment, like the tundra where the soil is frozen,
bryophytes grow well because they do not have roots and can dry and
rehydrate rapidly once water is again available. Mosses are at the base of
the food chain in the tundra biome. Many species—from small insects to
musk oxen and reindeer—depend on mosses for food. In turn, predators
feed on the herbivores, which are the primary consumers. Some reports
indicate that bryophytes make the soil more amenable to colonization by
other plants. Because they establish symbiotic relationships with nitrogen-
fixing cyanobacteria, mosses replenish the soil with nitrogen.
At the end of the nineteenth century, scientists observed that lichens and
mosses were becoming increasingly rare in urban and suburban areas. Since
bryophytes have neither a root system for absorption of water and nutrients,
nor a cuticle layer that protects them from desiccation, pollutants in
rainwater readily penetrate their tissues; they absorb moisture and nutrients
through their entire exposed surfaces. Therefore, pollutants dissolved in
rainwater penetrate plant tissues readily and have a larger impact on mosses
than on other plants. The disappearance of mosses can be considered a
bioindicator for the level of pollution in the environment.
Ferns contribute to the environment by promoting the weathering of rock,
accelerating the formation of topsoil, and slowing down erosion by
spreading rhizomes in the soil. The water ferns of the genus Azolla harbor
nitrogen-fixing cyanobacteria and restore this important nutrient to aquatic
habitats.
Seedless plants have historically played a role in human life through use as
tools, fuel, and medicine. Dried peat moss, Sphagnum, is commonly used as
fuel in some parts of Europe and is considered a renewable resource.
Sphagnum bogs ([link]) are cultivated with cranberry and blueberry bushes.
The ability of Sphagnum to hold moisture makes the moss a common soil
conditioner. Florists use blocks of Sphagnum to maintain moisture for floral
arrangements.
Sphagnum acutifolium is dried
peat moss and can be used as
fuel. (credit: Ken Goulding)
The attractive fronds of ferns make them a favorite ornamental plant.
Because they thrive in low light, they are well suited as house plants. More
importantly, fiddleheads are a traditional spring food of Native Americans
in the Pacific Northwest, and are popular as a side dish in French cuisine.
The licorice fern, Polypodium glycyrrhiza, is part of the diet of the Pacific
Northwest coastal tribes, owing in part to the sweetness of its rhizomes. It
has a faint licorice taste and serves as a sweetener. The rhizome is also
valued by Native Americans for its medicinal properties and is used as a
remedy for sore throat.
By far the greatest impact of seedless vascular plants on human life,
however, comes from their extinct progenitors. The tall club mosses,
horsetails, and tree-like ferns that flourished in the swampy forests of the
Carboniferous period gave rise to large deposits of coal throughout the
world. Coal provided an abundant source of energy during the Industrial
Revolution, which had tremendous consequences on human societies,
including rapid technological progress and growth of large cities, as well as
the degradation of the environment. Coal is still a prime source of energy
and also a major contributor to global warming.
Evolution of Seed Plants
Introduction
" T was aware of Darwin's views fourteen years before I adopted them and I
have done so solely and entirely from an independent study of the plants
themselves. " Sir Joseph Dalton Hooker, letter to E.H. Harvey, in L. Huxley,
Life and Letters of Sir Joseph Dalton Hooker (1918)
The evolution of plants is indeed well-understood, and Hooker's recognition
of the usefulness of evolutionary theory in understanding plant biology was
correct. The first plants to colonize land were most likely closely related to
modern day mosses (bryophytes) and are thought to have appeared about
500 million years ago, based on fossil and DNA sequence evidence. They
were followed by liverworts (also bryophytes) and primitive vascular plants
—the pterophytes—from which modern ferns are derived. Like
gymnosperms and angiosperms, the life cycle of bryophytes and
pterophytes is characterized by the alternation of generations. What sets
bryophytes and pterophytes apart from gymnosperms and angiosperms is
their reproductive requirement for water. The completion of the bryophyte
and pterophyte life cycle requires water because the male gametophyte
releases sperm, which must swim—propelled by their flagella—to reach
and fertilize the female gamete or egg. After fertilization, the zygote
matures and grows into a sporophyte, which in turn will form sporangia or
"spore vessels." In the sporangia, mother cells undergo meiosis and produce
the haploid spores. Release of spores in a suitable environment will lead to
germination and a new generation of gametophytes.
In seed plants, the evolutionary trend led to a dominant sporophyte
generation, and at the same time, a systematic reduction in the size of the
gametophyte: from a conspicuous structure to a microscopic cluster of cells
enclosed in the tissues of the sporophyte. The gametophyte is thus
dependent on the sporophyte for shelter and nutrition. Whereas lower
vascular plants, such as club mosses and ferns, are mostly homosporous
(produce only one type of spore), all seed plants are heterosporous. They
form two types of spores: megaspores (female) and microspores (male).
Megaspores develop into female gametophytes that produce eggs, and
microspores mature into male gametophytes that generate sperm. Because
the gametophytes mature within the sporophyte, they are not free-living, as
are the gametophytes of other seedless vascular plants. Heterosporous
seedless plants are seen as the evolutionary forerunners of seed plants.
Seeds and pollen—two critical adaptations to drought, and to reproduction
that doesn’t require water—distinguish seed plants from other (seedless)
vascular plants. Both adaptations were required for the colonization of land
begun by the bryophytes and their ancestors. Fossils place the earliest
distinct seed plants at about 350 million years ago. The first reliable record
of gymnosperms dates their appearance to the late Paleozoic, about 319
million years ago ([link]). Gymnosperms were preceded by
progymnosperms, the first naked seed plants, which arose about 380 million
years ago. Progymnosperms were a transitional group of plants that
superficially resembled conifers (cone bearers) because they produced
wood from the secondary growth of vascular tissues; however, they still
reproduced like ferns, releasing spores into the environment. Gymnosperms
dominated the landscape in the early and middle Mesozoic era.
Angiosperms surpassed gymnosperms by about 100 million years ago in the
late Mesozoic era, and today are the most abundant plant group in most
terrestrial biomes.
Flowers and Fruits
Angiosperms
Seeds Gnetophytes
Conifers
Vascular Gymnosperms
Ginkgos
Tissue Cycads
Whisk ferns | Vascular
True ferns
Horsetails Seedless
Club mosses
Land
Plants
Mosses
Hornworts Bryophytes
Liverworts
500 400 300 200 100 0
Time (millions of year ago)
Phylogeny of the land plants with the major adaptation for living on
land. Note the geological eras along the bottom. Work by Robert A.
Bear
Pollen and seed were adaptations that allowed seed plants to break their
dependence on water for reproduction and development of the embryo, and
to conquer dry land. The pollen grains are the male gametophytes, which
contain the sperm (gametes) of the plant. The small haploid (1N) cells are
encased in a protective coat that prevents desiccation (drying out) and
mechanical damage. Pollen grains can travel far from their original
sporophyte, spreading the plant’s genes. The seed offers the embryo
protection, nourishment, and a mechanism to maintain dormancy for tens or
even thousands of years, ensuring germination can occur when growth
conditions are optimal. Seeds therefore allow plants to disperse the next
generation through both space and time. With such evolutionary
advantages, seed plants have become the most successful and familiar
group of plants, in part because of their size and striking appearance.
Evolution of Gymnosperms
The fossil plant Elkinsia polymorpha, a "seed fern" from the Devonian
period—about 400 million years ago—is considered the earliest seed plant
known to date. Seed ferns ((link]) produced seeds along their branches
without specialized structures. What makes them the first true seed plants is
that they developed structures to enclose and protect the ovule—the female
gametophyte and associated tissues—which develops into a seed upon
fertilization. Seed plants resembling modern tree ferns became more
numerous and diverse in the coal swamps of the Carboniferous period.
This fossilized leaf is from
Glossopteris, a seed fern that thrived
during the Permian age (290—
240 million years ago). (credit: D.L.
Schmidt, USGS)
Fossil records indicate the first gymnosperms (progymnosperms) most
likely originated in the Paleozoic era, during the middle Devonian period:
about 390 million years ago. Following the wet Mississippian and
Pennsylvanian periods, which were dominated by giant fern trees, the
Permian period was dry. This gave a reproductive edge to seed plants,
which are better adapted to survive dry spells. The Ginkgoales, a group of
gymnosperms with only one surviving species— Gingko biloba—were the
first gymnosperms to appear during the lower Jurassic. Gymnosperms
expanded in the Mesozoic era (about 240 million years ago), supplanting
ferns in the landscape, and reaching their greatest diversity during this time.
The Jurassic period was as much the age of the cycads (palm-tree-like
gymnosperms) as the age of the dinosaurs. Gingkoales and more familiar
conifers also dotted the landscape. Although angiosperms (flowering plants)
are the major form of plant life in most biomes, gymnosperms still
dominate some ecosystems, such as the taiga (boreal forests) and the alpine
forests at higher mountain elevations ({link]) because of their adaptation to
cold and dry growth conditions.
This boreal forest (taiga) has low-
lying plants and conifer trees.
(credit: L.B. Brubaker, NOAA)
Seeds and Pollen as an Evolutionary Adaptation to Dry Land
Unlike bryophyte and fern spores (which are haploid cells dependent on
moisture for rapid development of gametophytes), seeds contain a diploid
embryo that will germinate into a sporophyte. Storage tissue to sustain
growth and a protective coat give seeds their superior evolutionary
advantage. Several layers of hardened tissue prevent desiccation, and free
reproduction from the need for a constant supply of water. Furthermore,
seeds remain in a state of dormancy—induced by desiccation and the
hormone abscisic acid—until conditions for growth become favorable.
Whether blown by the wind, floating on water, or carried away by animals,
seeds are scattered in an expanding geographic range, thus avoiding
competition with the parent plant.
Pollen grains ({link]) are male gametophytes and are carried by wind, water,
or a pollinator. The whole structure is protected from desiccation and can
reach the female organs without dependence on water. Male gametes reach
female gametophyte and the egg cell though a pollen tube: an extension of a
cell within the pollen grain. The sperm of modern gymnosperms lack
flagella, but in cycads and the Gingko, the sperm still possess flagella that
allow them to swim down the pollen tube to the female gamete; however,
they are enclosed in a pollen grain.
< ‘
\
ie
Fy}
Cs bor
be
This fossilized pollen is from
a Buckbean fen core found in
Yellowstone National Park,
Wyoming. The pollen is
magnified 1,054 times.
(credit: R.G. Baker, USGS;
scale-bar data from Matt
Russell)
10m
Evolution of Angiosperms
Undisputed fossil records place the massive appearance and diversification
of angiosperms in the middle to late Mesozoic era. Angiosperms (“seed in a
vessel”) produce a flower containing male and/or female reproductive
structures. Fossil evidence ([link]) indicates that flowering plants first
appeared in the Lower Cretaceous, about 125 million years ago, and were
rapidly diversifying by the Middle Cretaceous, about 100 million years ago.
Earlier traces of angiosperms are scarce. Fossilized pollen recovered from
Jurassic geological material has been attributed to angiosperms. A few early
Cretaceous rocks show clear imprints of leaves resembling angiosperm
leaves. By the mid-Cretaceous, a staggering number of diverse flowering
plants crowd the fossil record. The same geological period is also marked
by the appearance of many modern groups of insects, including pollinating
insects that played a key role in ecology and the evolution of flowering
plants.
Although several hypotheses have been offered to explain this sudden
profusion and variety of flowering plants, none have garnered the consensus
of paleobotanists (scientists who study ancient plants). New data in
comparative genomics and paleobotany have, however, shed some light on
the evolution of angiosperms. The two adaptations of flowers and fruit
represent an improved reproductive strategy that served to protect the
embryo, while increasing genetic variability and range. Angiosperms did
not evolve from gymnosperms, but the groups do share a common ancestor
({link]).
The most primitive living angiosperm is considered to be Amborella
trichopoda, a small plant native to the rainforest of New Caledonia, an
island in the South Pacific. Analysis of the genome of A. trichopoda has
shown that it is related to all existing flowering plants and belongs to the
oldest confirmed branch of the angiosperm family tree. A few other
angiosperm groups called basal angiosperms, are viewed as primitive
because they branched off early from the phylogenetic tree. Most modern
angiosperms are Classified as either monocots or eudicots, based on the
structure of their leaves and embryos. Basal angiosperms, such as water
lilies, are considered more primitive because they share morphological
traits with both monocots and eudicots.
This leaf imprint shows
a Ficus speciosissima,
an angiosperm that
flourished during the
Cretaceous period.
(credit: W. T. Lee,
USGS)
Flowers and Fruits as an Evolutionary Adaptation
Angiosperms produce their gametes in separate organs, which are usually
housed in a flower. Both fertilization and embryo development take place
inside an anatomical structure that provides a stable system of sexual
reproduction largely sheltered from environmental fluctuations. Flowering
plants are the most diverse phylum on Earth after insects (Arthropoda);
flowers come in a bewildering array of sizes, shapes, colors, smells, and
arrangements. Most flowers have a mutualistic pollinator, with the
distinctive features of flowers reflecting the nature of the pollination agent.
The relationship between pollinator and flower characteristics is one of the
great examples of coevolution.
Following fertilization of the egg, the ovule grows into a seed. The
surrounding tissues of the ovary thicken, developing into a fruit that will
protect the seed and often ensure its dispersal over a wide geographic range.
Not all fruits develop from an ovary; such structures are “false fruits.” Like
flowers, fruit can vary tremendously in appearance, size, smell, and taste.
Tomatoes, walnut shells and avocados are all examples of fruit. As with
pollen and seeds, fruits also act as agents of dispersal. Some may be carried
away by the wind. Many attract animals that will eat the fruit and pass the
seeds through their digestive systems, then deposit the seeds in another
location. Cockleburs are covered with stiff, hooked spines that can hook
into fur (or clothing) and hitch a ride on an animal for long distances. The
cockleburs that clung to the velvet trousers of an enterprising Swiss hiker,
George de Mestral, inspired his invention of the loop and hook fastener he
named Velcro.
Gymnosperms
Introduction
" Tt took more than three thousand years to make some of the trees in these
westem woods ... Through all the wonderful, eventful centuries since
Christ's time—and long before that—God has cared for these trees, saved
them from drought, disease, avalanches, and a thousand straining, leveling
tempests and floods; but he cannot save them from fools." John Muir, in
"The American Forests", Atlantic Monthly (Aug 1897)
Giant Sequoia —
The Grizzly Giant, a Giant Sequoia
(Sequoiadendron giganteum) in the
Mariposa Grove of Yosemite National
Park. John Muir and others petitioned the
US Congress, resulting in the creation of
Yosemite and Sequoia National Parks in
1890. Photo by David A. Rintoul.
The redwood trees and Douglas firs referred to in Muir's quote are indeed
ancient, and among the largest living things on the planet. They are
members of the group we call gymnosperms, meaning “naked seeds,”
which are a diverse group of seed plants and are paraphyletic. Paraphyletic
groups are those in which not all members are descendants of a single
common ancestor. Gymnosperm characteristics include naked seeds (not
enclosed in an ovary), separate female and male gametes, pollination by
wind, and tracheids (which transport water and solutes in the vascular
system).
Gymnosperm seeds are not enclosed in an ovary (they are "naked"); rather,
they are exposed on cones or modified leaves. Gymnosperms were the
dominant phylum in the Mesozoic era. They are adapted to live where fresh
water is scarce during part of the year, or in the nitrogen-poor soil of a bog.
Therefore, they are still the prominent phylum in the coniferous biome or
taiga, where the evergreen conifers have a selective advantage in cold and
dry weather. Evergreen conifers continue low levels of photosynthesis
during the cold months, and are ready to take advantage of the first sunny
days of spring. One disadvantage is that conifers are more susceptible than
deciduous trees to infestations because conifers do not lose their leaves all
at once. They cannot, therefore, shed parasites and restart with a fresh
supply of leaves in spring.
The life cycle of a gymnosperm involves alternation of generations, with a
dominant sporophyte and reduced gametophytes that resides within the
sporophyte. All gymnosperms are heterosporous. The male and female
reproductive organs can form in cones (strobili). Male and female sporangia
are produced either on the same plant, described as monoecious (“one
home”), or on separate plants, referred to as dioecious (“two homes”)
plants. The life cycle of a conifer will serve as our example of reproduction
in gymnosperms.
Life Cycle of a Conifer
Pine trees are conifers (cone bearing) and carry both male and female
sporophylls on the same mature sporophyte. Therefore, they are
monoecious plants. Like all gymnosperms, pines are heterosporous and
generate two different types of spores: male microspores and female
megaspores. In the male or staminate cones, the microsporocytes give rise
to pollen grains by meiosis. In the spring, large amounts of yellow pollen
are released and carried by the wind. Some gametophytes will land on a
female cone. Pollination is defined as the initiation of pollen tube growth.
The pollen tube develops slowly, and the generative cell in the pollen grain
divides into two haploid sperm cells by mitosis. At fertilization, one of the
sperm cells will finally unite its haploid nucleus with the haploid nucleus of
a haploid egg cell.
Female cones contain two ovules per scale. One megaspore mother cell, or
megasporocyte, undergoes meiosis in each ovule. Three of the four cells
break down; only a single surviving cell will develop into a female
multicellular gametophyte, which encloses one or more archegonia (an
archegonium is a reproductive organ that contains a single large egg). Upon
fertilization, the resulting diploid zygote will give rise to the embryo, which
is enclosed in a seed coat of tissue from the parent plant. Fertilization and
seed development is a long process in pine trees: it may take up to two
years after pollination. The seed that is formed contains three generations of
tissues: the seed coat that originates from the sporophyte tissue, the
gametophyte that will provide nutrients, and the embryo itself.
[link] illustrates the life cycle of a conifer. The sporophyte (2N) phase is the
longest phase in the life of a gymnosperm. The gametophytes (1N)—
microspores and megaspores—are reduced in size. It may take more than
year between pollination and fertilization while the pollen tube grows
towards the megasporocyte (2N), which undergoes meiosis into
megaspores. The megaspores will mature into female gametophytes that
then produce eggs (1N).
Gymnosperm Life Cycle
ee ere ~ ee §,.& Male Gametophyte (Pollen)
oe Se
Microspores Mitosis © Pollination so”
P'S a7
This image shows the life cycle of a conifer. Pollen from male cones
blows up into upper branches, where it fertilizes female cones. Work
by Eva Horne and Robert A. Bear
Diversity of Gymnosperms
Modern gymnosperms are classified into four phyla. Coniferophyta,
Cycadophyta, and Ginkgophyta are similar in their production of secondary
cambium (cells that generate the vascular system of the trunk or stem and
are partially specialized for water transportation) and their pattern of seed
development. However, the three phyla are not closely related
phylogenetically to each other. Gnetophyta are considered the closest group
to angiosperms because they produce true xylem tissue.
Conifers (Coniferophyta)
Conifers are the dominant phylum of gymnosperms, with the most variety
of species ([link]). Most are typically tall trees that usually bear scale-like
or needle-like leaves. Water evaporation from leaves is reduced by their thin
shape and the thick cuticle. Snow slides easily off needle-shaped leaves,
keeping the load light and decreasing breaking of branches. Adaptations to
cold and dry weather explain the predominance of conifers at high altitudes
and in cold climates. Conifers include familiar evergreen trees such as
pines, spruces, firs, cedars, sequoias, and yews. A few species are
deciduous and lose their leaves in fall. The European larch and the tamarack
are examples of deciduous conifers ([link]d). Many coniferous trees are
harvested for paper pulp and timber. The wood of conifers is more primitive
than the wood of angiosperms; it contains tracheids, but no vessel elements,
and is therefore referred to as “soft wood.”
Conifers are the dominant form of vegetation
in cold or arid environments and at high
altitudes. Shown here are the (a) evergreen
spruce Picea sp., (b) juniper Juniperus sp., (c)
coast redwood Sequoia sempervirens, which is
a deciduous gymnosperm, and (d) the tamarack
Larix larcinia. Notice the yellow leaves of the
tamarack. (credit a: modification of work by
Rosendahl; credit b: modification of work by
Alan Levine; credit c: modification of work by
Wendy McCormic; credit d: modification of
work by Micky Zlimen)
Cycads
Cycads thrive in mild climates, and are often mistaken for palms because of
the shape of their large, compound leaves. Cycads bear large cones ((link]),
and may be pollinated by beetles rather than wind: unusual for a
gymnosperm. They dominated the landscape during the age of dinosaurs in
the Mesozoic, but only a hundred or so species persisted to modern times.
They face possible extinction, and several species are protected through
international conventions. Because of their attractive shape, they are often
used as ornamental plants in gardens in the tropics and subtropics.
This Encephalartos ferox cycad
has large cones and broad, fern-
like leaves. (credit: Wendy Cutler)
Gingkophytes
The single surviving species of Gingkophytes is the Gingko biloba ({link)).
Its fan-shaped leaves—unique among seed plants because they feature a
dichotomous venation pattern—turn yellow in autumn and fall from the
tree. For centuries, G. biloba was cultivated by Chinese Buddhist monks in
monasteries, which ensured its preservation. It is planted in public spaces
because it is unusually resistant to pollution. Male and female organs are
produced on separate plants. Typically, gardeners plant only male trees
because the seeds produced by the female plant have an off-putting smell of
rancid butter.
Th 30,
This plate from the 1870
book Flora Japonica, Sectio
Prima (Tafelband) depicts the
leaves and fruit of Gingko
biloba, as drawn by Philipp
Franz von Siebold and Joseph
Gerhard Zuccarini.
Gnetophytes
Gnetophytes are the closest relative to modern angiosperms, and include
three dissimilar genera of plants: Ephedra, Gnetum, and Welwitschia
({link]). Like angiosperms, they have broad leaves. In tropical and
subtropical zones, gnetophytes are vines or small shrubs. Ephedra occurs in
dry areas of the West Coast of the United States and Mexico. Ephedra’s
small, scale-like leaves are the source of the compound ephedrine, which is
used in medicine as a potent decongestant. Because ephedrine is similar to
amphetamines, both in chemical structure and neurological effects, its use is
restricted to prescription drugs. Like angiosperms, but unlike other
gymnosperms, all gnetophytes possess vessel elements in their xylem.
(a) Ephedra (b) Gnetum (c) Welwitschia
(a) Ephedra viridis, known by the common name Mormon tea,
grows on the West Coast of the United States and Mexico. (b)
Gnetum gnemon grows in Malaysia. (c) The large Welwitschia
mirabilis can be found in the Namibian desert. (credit a:
modification of work by USDA; credit b: modification of work
by Malcolm Manners; credit c: modification of work by Derek
Keats)
Angiosperms
Introduction
"The ginkgo tree is from the era of dinosaurs, but while the dinosaur has
been extinguished, the modern ginkgo has not changed. After the atomic
bomb in Hiroshima, the ginkgo was the first tree that came up. It’s
amazing." Koji Nakanishi, organic chemist (2013)
From their humble and still obscure beginning during the early Jurassic
period, the angiosperms—or flowering plants—have evolved to dominate
most terrestrial ecosystems ([link]). With more than 250,000 species, the
angiosperm phylum (Anthophyta) is second only to insects in terms of
diversification.
4
These flowers grow in a botanical
garden border in Bellevue, WA.
Flowering plants dominate terrestrial
landscapes. The vivid colors of
flowers are an adaptation to
pollination by animals such as insects
and birds. (credit: Myriam Feldman)
The success of angiosperms is due to two novel reproductive structures:
flowers and fruit. The function of the flower is to ensure pollination.
Flowers also provide protection for the ovule and developing embryo inside
a receptacle. The function of the fruit is seed dispersal. They also protect
the developing seed. Different fruit structures or tissues on fruit—such as
sweet flesh, wings, parachutes, or spines that grab—reflect the dispersal
strategies that help spread seeds.
Flowers
Flowers are modified leaves, or sporophylls, organized around a central
stalk. Although they vary greatly in appearance, all flowers contain the
Same structures: sepals, petals, carpels, and stamens. The receptacle
attaches the flower to the plant. A whorl of sepals (collectively called the
calyx) is located at the base of the peduncle (stem of the flower) and
encloses the unopened floral bud. Sepals are usually photosynthetic organs,
although there are some exceptions. For example, the corolla in lilies and
tulips consists of three sepals and three petals that look virtually identical.
Petals, collectively the corolla, are located inside the whorl of sepals and
often display vivid colors to attract pollinators. Flowers pollinated by wind
are usually small, feathery, and visually inconspicuous. The sexual organs
(carpels and stamens) are located at the center of the flower.
As illustrated in [link], styles, stigmas, and ovules constitute the female
organ: the carpel. Flower structure is very diverse, and carpels may be
singular, multiple, or fused. Multiple fused carpels comprise a pistil. The
megaspores and the female gametophytes are produced and protected by the
thick tissues of the carpel. A long, thin structure called a style leads from
the sticky stigma, where pollen is deposited, to the ovary, enclosed in the
carpel. The ovary houses one or more ovules, each of which will develop
into a seed upon fertilization. The male reproductive organs, the stamens,
surround the central carpel. Stamens are composed of a thin stalk called a
filament and a sac-like structure called the anther. The filament supports
the anther, where the microspores are produced by meiosis and develop
into pollen grains.
Stamens
Petal
Flower
Corolla (composed of petals)
Calyx (composed of sepals)
This image depicts the structure of a
perfect flower. Perfect flowers produce
both male and female floral organs. The
flower shown has only one carpel, but
some flowers have a cluster of carpels.
Together, all the carpels make up the
pistil. (credit: modification of work by
Mariana Ruiz Villareal)
Fruit
As the seed develops, the walls of the ovary thicken and form the fruit. The
seed forms in an ovary, which also enlarges as the seeds grow. In botany, a
fertilized and fully grown, ripened ovary is a fruit. Many foods commonly
called vegetables are actually fruit. Eggplants, zucchini, string beans, and
bell peppers are all technically fruit because they contain seeds and are
derived from the thick ovary tissue. Acorns (a nut), and winged maple
whirligigs (whose botanical name is samara) are also fruit. Botanists
classify fruit into more than two dozen different categories, only a few of
which are actually fleshy and sweet.
Mature fruit can be fleshy or dry. Fleshy fruit include the familiar berries,
peaches, apples, grapes, and tomatoes. Rice, wheat, and nuts are examples
of dry fruit. Another distinction is that not all fruits are derived from the
ovary. For instance, strawberries are derived from the receptacle and in
apples the receptacle forms the pericarp or the fleshy part. Some fruits are
derived from separate ovaries in a single flower, such as the raspberry.
Other fruits, such as the pineapple, form from clusters of flowers.
Additionally, some fruits, like watermelon and orange, have rinds.
Regardless of how they are formed, fruits are an agent of seed dispersal.
The variety of shapes and characteristics reflect the mode of dispersal.
Wind carries the light dry fruit of trees and dandelions. Water transports
floating coconuts. Some fruits attract herbivores with color or perfume, or
as food. Once eaten, tough, undigested seeds are dispersed through the
herbivore’s feces. Other fruits have burs and hooks to cling to fur and hitch
rides on animals.
The Life Cycle of an Angiosperm
The sporophyte phase is the main phase of an angiosperm’s life cycle
({link]). Like gymnosperms, angiosperms are heterosporous. Therefore,
they generate microspores, which will generate pollen grains as the male
gametophytes, and megaspores, which will form an ovule that contains
female gametophytes. Inside the anthers’ microsporangia, male
gametophytes divide by meiosis to generate haploid microspores, which, in
turn, undergo mitosis and give rise to pollen grains. Each pollen grain
contains two cells: one generative cell that will divide into two sperm and a
second cell that will become the pollen tube cell.
Note:
Angiosperm Life Cycle
R a fed
Tr yy Fer
(5D) a.
i
f'
The life cycle of an angiosperm is shown. Anthers and carpels are
structures that shelter the actual gametophytes: the pollen grain and
embryo sac. Work by Eva Horne and Robert A. Bear
Within the ovule, sheltered within the ovary of the carpel, a cell undergoes
meiosis, generating four megaspores—three small and one large. Only the
large megaspore survives; it divides to produce the female gametophyte.
The megaspore divides three times to form an eight-cell stage. Three of
these cells migrate to each pole of the embryo sac while two come to the
equator. These two cells will fuse to form one central cell with two haploid
polar nuclei. The two cells closest to the egg are called synergids; the three
cells on the opposite end of the gametophyte are called antipodals.
Pollen grains are the male gametophytes. When a pollen grain reaches the
stigma, a pollen tube extends from the grain, grows down the style, and
enters through the micropyle: an opening in the outer covering of the ovule.
Two sperm cells travel down this tube and enter the ovule.
A double fertilization event then occurs. One sperm combines with the egg,
forming a diploid zygote—the future embryo. The other sperm fuses with
the two polar nuclei, forming a triploid (3n) cell that will develop into the
endosperm, which is tissue that serves as a food reserve. The zygote
develops into an embryo with a radicle, or small root, and one (monocot) or
two (dicot) leaf-like organs called cotyledons. This difference in the number
of embryonic leaves is the basis for the two major groups of angiosperms:
the monocots and the eudicots. Seed food reserves are stored outside the
embryo, in the form of complex carbohydrates, lipids, or proteins. The
cotyledons serve as conduits to transmit the broken-down food reserves
from their storage site inside the seed to the developing embryo. The seed
consists of a toughened layer of integuments (the seed coat), the endosperm
with food reserves, and at the center, the well-protected embryo.
Most flowers are monoecious, which means that they carry both stamens
and carpels. Monoecious flowers are also known as “perfect” flowers
because they contain both types of sex organs. However, only a few species
self-pollinate. Both anatomical and environmental barriers promote
pollination between different individuals (cross-pollination) mediated by a
physical agent (wind or water), or an animal, such as an insect or bird.
Cross-pollination increases genetic diversity in a species.
Diversity of Angiosperms
Angiosperms are classified in a single phylum: the Anthophyta. Modern
angiosperms appear to be a monophyletic group, which means that they
originate from a single ancestor. Flowering plants are divided into two
major groups, according to the structure of the cotyledons, pollen grains,
and other structures. Monocots include grasses and lilies, and eudicots
form a polyphyletic group. Basal angiosperms are a group of plants that
are believed to have branched off before the separation into monocots and
eudicots because they exhibit traits from both groups. They are categorized
separately in many classification schemes. The Magnoliidae (magnolia
trees, laurels, and water lilies) and the Piperaceae (peppers) belong to the
basal angiosperm group.
Basal Angiosperms
The Magnoliidae are represented by the magnolias: tall trees bearing large,
fragrant flowers that have many parts and are considered archaic ({link]d).
Laurel trees produce fragrant leaves and small, inconspicuous flowers. The
Laurales grow mostly in warmer climates and are small trees and shrubs.
Familiar plants in this group include the bay laurel, cinnamon, spice bush
({link]a), and avocado tree. The Nymphaeales are comprised of the water
lilies, lotus ({link]c), and similar plants; all species thrive in freshwater
biomes, and have leaves that float on the water surface or grow underwater.
Water lilies are particularly prized by gardeners, and have graced ponds and
pools for thousands of years. The Piperales are a group of herbs, shrubs,
and small trees that grow in the tropical climates. They have small flowers
without petals that are tightly arranged in long spikes. Many species are the
source of prized fragrance or spices, for example the berries of Piper
nigrum ((link]b) are the familiar black peppercorns that are used to flavor
many dishes.
The (a) common spicebush belongs to
the Laurales, the same family as
cinnamon and bay laurel. The fruit of
(b) the Piper nigrum plant is black
pepper, the main product that was
traded along spice routes. Notice the
small, unobtrusive, clustered flowers.
(c) Lotus flowers, Nelumbo nucifera,
have been cultivated since ancient
times for their ornamental value; the
root of the lotus flower is eaten as a
vegetable. The red seeds of (d) a
magnolia tree, characteristic of the
final stage, are just starting to appear.
(credit a: modification of work by
Cory Zanker; credit b: modification
of work by Franz Eugen Kohler;
credit c: modification of work by
"berduchwal"/Flickr; credit d:
modification of work by
"Coastside2"/Wikimedia Commons).
Monocots
Plants in the monocot group are primarily identified as such by the presence
of a single cotyledon in the seedling. Other anatomical features shared by
monocots include veins that run parallel to the length of the leaves, and
flower parts that are arranged in a three- or six-fold symmetry. In monocots,
the vascular tissue is scattered in the stem. True woody tissue is rarely
found in monocots. In palm trees, vascular and parenchyma tissues
produced by the primary and secondary thickening meristems form the
trunk. The pollen from the first angiosperms was monosulcate, containing a
single furrow or pore through the outer layer. This feature is still seen in the
modern monocots. Vascular tissue of the stem is not arranged in any
particular pattern. The root system is mostly adventitious and unusually
positioned, with no major tap root. The monocots include familiar plants
such as the true lilies (which are at the origin of their alternate name of
Liliopsida), orchids, grasses, and palms. Many important crops are
monocots, such as rice and other cereals, corn, sugar cane, and tropical
fruits like bananas and pineapples ([link]).
Monocots
(a) Rice (b) Wheat (c) Bananas
Dicots
d) Cabbage ‘e) Beans Peaches
9)
The world’s major crops are flowering plants. (a)
Rice, (b) wheat, and (c) bananas are monocots, while
(d) cabbage, (e) beans, and (f) peaches are eudicots.
(credit a: modification of work by David Nance,
USDA ARS; credit b, c: modification of work by
Rosendahl; credit d: modification of work by Bill
Tarpenning, USDA; credit e: modification of work by
Scott Bauer, USDA ARS; credit f: modification of
work by Keith Weller, USDA)
Eudicots
Eudicots, or true dicots, are characterized by the presence of two cotyledons
in the developing shoot. Veins form a network in leaves, and flower parts
come in four, five, or many whorls. Vascular tissue forms a ring in the stem.
Eudicots can be herbaceous, or produce woody tissues. Most eudicots
produce pollen that is trisulcate or triporate, with three furrows or pores.
The root system is usually anchored by one main root. Eudicots comprise
two-thirds of all flowering plants. The major differences between monocots
and eudicots are summarized in [link]. Many species exhibit characteristics
that belong to either group; as such, the classification of a plant as a
monocot or a eudicot is not always clearly evident.
Comparison of Structural Characteristics of Monocots and
Eudicots
Characteristic
Cotyledon
Veins in
Leaves
Stem Vascular
Tissue
Roots
Root Vascular
Tissues
Pollen
Flower Parts
Monocot
One
Parallel
Scattered
Network of
adventitious roots
Xylem in ring
pattern
Single pore or
furrow
Multiples of three
Eudicot
Two
Network (branched)
Arranged in ring pattern
Tap root with many
lateral roots
Xylem in X or star
pattern
Three pores or furrows
Multiples of four or five
and whorls
Asexual Reproduction
Introduction
" From the sexual, or amatorial, generation of plants new varieties, or
improvements, are frequently obtained; as many of the young plants from
seeds are dissimilar to the parent, and some of them superior to the parent in
the qualities we wish to possess... Sexual reproduction is the chef d'oeuvre,
the master-piece of nature." Erasmus Darwin, English physician and
grandfather of Charles Darwin, in Phytologia, (1800)
Sexual reproduction is certainly one way to produce the next generation,
but it is not the only way. And in some situations, it might not be the best
way. Many plants are able to propagate themselves using asexual
reproduction by simply growing a new individual by mitosis. This method
does not require the investment required to produce a flower, attract
pollinators, or find a means of seed dispersal. Asexual reproduction
produces plants that are genetically identical to the parent plant because no
mixing of male and female gametes takes place. Traditionally, these plants
survive well under stable environmental conditions when compared with
plants produced from sexual reproduction because they carry genes
identical to those of their parents.
Many different structures facilitate asexual reproduction ({link]). Garlic and
gladiolus have an underground stem called a corm. Bulbs, such as a scaly
bulb in lilies and a tunicate bulb in daffodils, are other common examples.
A potato is a stem tuber, while parsnip propagates from a taproot. Ginger
and iris produce rhizomes, while ivy uses an adventitious root (a root
arising from a plant part other than the main or primary root), and the
strawberry plant has a stolon, which is also called a runner. In each case, the
tissue was grown via mitosis and becomes a new individual when separated
from the 'parent' plant.
Different types of stems allow
for asexual reproduction. (a)
The corm of a garlic plant looks
similar to (b) a tulip bulb, but
the corm is solid tissue, while
the bulb consists of layers of
modified leaves that surround
an underground stem. Both
corms and bulbs can self-
propagate, giving rise to new
plants. (c) Ginger forms masses
of stems called rhizomes that
can give rise to multiple plants.
(d) Potato plants form fleshy
stem tubers. Each eye in the
stem tuber can give rise toa
new plant. (e) Strawberry plants
form stolons: stems that grow at
the soil surface or just below
ground and can give rise to new
plants. (credit a: modification of
work by Dwight Sipler; credit c:
modification of work by Albert
Cahalan, USDA ARS; credit d:
modification of work by
Richard North; credit e:
modification of work by Julie
Magro)
Some plants can produce seeds without fertilization. Either the ovule or part
of the ovary, which is diploid in nature, gives rise to a new seed. This
method of reproduction is known as apomixis.
One advantage of asexual reproduction is that the resulting plant will reach
maturity faster. Since the new plant is arising from an adult plant or plant
parts, it will also be sturdier than a seedling. Asexual reproduction can take
place by natural or artificial (assisted by humans) means.
Natural Methods of Asexual Reproduction
Natural methods of asexual reproduction include strategies listed above that
plants have developed to self-propagate. Many plants—like ginger, onion,
gladioli, and dahlia—continue to grow from buds that are present on the
surface of the stem. In some plants, such as the sweet potato, adventitious
roots or runners can give rise to new plants [link]. In Bryophyllum and
kalanchoe, the leaves have small buds on their margins. When these are
detached from the plant, they grow into independent plants; or, they may
start growing into independent plants if the leaf touches the soil. Some
plants can be propagated through cuttings alone.
Stolon
(runner)
A stolon, or runner, is a stem
that runs along the ground. At
the nodes, it forms adventitious
roots and buds that grow into a
new plant.
Artificial Methods of Asexual Reproduction
These methods are frequently employed to give rise to new, and sometimes
novel, plants. They include grafting, cutting, layering, and
micropropagation.
Grafting
Grafting has long been used to produce novel varieties of roses, citrus
species, and other plants. In grafting, two plant species are used; part of the
stem of the desirable plant is grafted onto a rooted plant called the stock.
The part that is grafted or attached is called the scion. Both are cut at an
oblique angle (any angle other than a right angle), placed in close contact
with each other, and are then held together [link]. Matching up these two
surfaces as closely as possible is extremely important because these will be
holding the plant together. The vascular systems of the two plants grow and
fuse, forming a graft. After a period of time, the scion starts producing
shoots, and eventually starts bearing flowers and fruits. Grafting is widely
used in viticulture (grape growing) and the citrus industry. Scions capable
of producing a particular fruit variety are grafted onto root stock with
specific resistance to disease.
Grafting is an artificial method of
asexual reproduction used to
produce plants combining
favorable stem characteristics with
favorable root characteristics. The
stem of the plant to be grafted is
known as the scion, and the root is
called the stock.
Cutting
Plants such as coleus and money plant are propagated through stem
cuttings, where a portion of the stem containing nodes and internodes is
placed in moist soil and allowed to root. In some species, stems can start
producing a root even when placed only in water. For example, leaves of
the African violet will root if kept in water undisturbed for several weeks.
Layering
Layering is a method in which a stem attached to the plant is bent and
covered with soil. Young stems that can be bent easily without any injury
are preferred. Jasmine and bougainvillea (paper flower) can be propagated
this way [link]. In some plants, a modified form of layering known as air
layering is employed. A portion of the bark or outermost covering of the
stem is removed and covered with moss, which is then taped. Some
gardeners also apply rooting hormone. After some time, roots will appear,
and this portion of the plant can be removed and transplanted into a separate
pot.
In layering, a part of the stem is
buried so that it forms a new plant.
(credit: modification of work by
Pearson Scott Foresman, donated
to the Wikimedia Foundation)
Micropropagation
Micropropagation (also called plant tissue culture) is a method of
propagating a large number of plants from a single plant in a short time
under laboratory conditions [link]. This method allows propagation of rare,
endangered species that may be difficult to grow under natural conditions,
are economically important, or are in demand as disease-free plants.
Micropropagation is used to
propagate plants in sterile
conditions. (credit: Nikhilesh
Sanyal)
To start plant tissue culture, a part of the plant such as a stem, leaf, embryo,
anther, or seed can be used. The plant material is thoroughly sterilized using
a combination of chemical treatments standardized for that species. Under
sterile conditions, the plant material is placed on a plant tissue culture
medium that contains all the minerals, vitamins, and hormones required by
the plant. The plant part often gives rise to an undifferentiated mass known
as Callus, from which individual plantlets begin to grow after a period of
time. These can be separated and are first grown under greenhouse
conditions before they are moved to field conditions.
Plant Life Spans
The length of time from the beginning of development to the death of a
plant is called its life span. The life cycle, on the other hand, is the sequence
of stages a plant goes through from seed germination to seed production of
the mature plant. Some plants, such as annuals, only need a few weeks to
grow, produce seeds and die. Other plants, such as the bristlecone pine, live
for thousands of years. Some bristlecone pines have a documented age of
4,500 years [link]. Even as some parts of a plant, such as regions containing
meristematic tissue—the area of active plant growth consisting of
undifferentiated cells capable of cell division—continue to grow, some parts
undergo programmed cell death (apoptosis). The cork found on stems, and
the water-conducting tissue of the xylem, for example, are composed of
dead cells.
The bristlecone pine, shown here in
the Ancient Bristlecone Pine Forest in
the White Mountains of eastern
California, has been known to live for
4,500 years. (credit: Rick Goldwaser)
Plant species that complete their lifecycle in one season are known as
annuals, an example of which is Arabidopsis, or mouse-ear cress. Biennials
such as carrots complete their lifecycle in two seasons. In a biennial’s first
season, the plant has a vegetative phase, whereas in the next season, it
completes its reproductive phase. Commercial growers harvest the carrot
roots after the first year of growth, and do not allow the plants to flower.
Perennials, such as the magnolia, complete their lifecycle in two years or
more.
In another classification based on flowering frequency, monocarpic plants
flower only once in their lifetime; examples include bamboo and yucca.
During the vegetative period of their life cycle (which may be as long as
120 years in some bamboo species), these plants may reproduce asexually
and accumulate a great deal of food material that will be required during
their once-in-a-lifetime flowering and setting of seed after fertilization.
Soon after flowering, these plants die. Polycarpic plants form flowers many
times during their lifetime. Fruit trees, such as apple and orange trees, are
polycarpic; they flower every year. Other polycarpic species, such as
perennials, flower several times during their life span, but not each year. By
this means, the plant does not require all its nutrients to be channeled
towards flowering each year.
As is the case with all living organisms, genetics and environmental
conditions have a role to play in determining how long a plant will live.
Susceptibility to disease, changing environmental conditions, drought, cold,
and competition for nutrients are some of the factors that determine the
survival of a plant. Plants continue to grow, despite the presence of dead
tissue such as cork. Individual parts of plants, such as flowers and leaves,
have different rates of survival. In many trees, the older leaves turn yellow
and eventually fall from the tree. Leaf fall is triggered by factors such as a
decrease in photosynthetic efficiency, due to shading by upper leaves, or
oxidative damage incurred as a result of photosynthetic reactions. The
components of the part to be shed are recycled by the plant for use in other
processes, such as development of seed and storage. This process is known
as nutrient recycling.
The aging of a plant and all the associated processes is known as
senescence, which is marked by several complex biochemical changes. One
of the characteristics of senescence is the breakdown of chloroplasts, which
is characterized by the yellowing of leaves. The chloroplasts contain
components of photosynthetic machinery such as membranes and proteins.
Chloroplasts also contain DNA. The proteins, lipids, and nucleic acids are
broken down by specific enzymes into smaller molecules and salvaged by
the plant to support the growth of other plant tissues.
The complex pathways of nutrient recycling within a plant are not well
understood. Hormones are known to play a role in senescence. Applications
of cytokinins and ethylene delay or prevent senescence; in contrast,
abscissic acid causes premature onset of senescence.
The Plant Body
Introduction
" A mile and a half from town, I came to a grove of tall cocoanut trees, with
clean, branchless stems reaching straight up sixty or seventy feet and
topped with a spray of green foliage sheltering clusters of cocoanuts—not
more picturesque than a forest of colossal ragged parasols, with bunches of
magnified grapes under them, would be. I once heard a grouty northern
invalid say that a cocoanut tree might be poetical, possibly it was; but it
looked like a feather-duster struck by lightning. I think that describes it
better than a picture—and yet, without any question, there is something
fascinating about a cocoanut tree—and graceful, too." Mark Twain,
Roughing it, (1913)
Palm tree on a tropical beach
Palm tree on a beach, Tulum, Mexico.
(Photo by David A. Rintoul)
Twain's observations about the "cocoanut tree" focuses on some of the more
obvious parts of a plant: the stem, the leaves, the seeds, etc. Some of the
other parts of a plant are less obvious, but not less important to the health
and well-being of the organism. Like animals, plants have organelles, cells,
tissues and organs.
Plant Organ Systems
In plants, just as in animals, similar cells working together form a tissue.
When different types of tissues work together to perform a unique function,
they form an organ; organs working together form organ systems. Vascular
plants have two distinct organ systems: a shoot system, and a root system.
The shoot system consists of two portions: the vegetative (non-
reproductive) parts of the plant, such as the leaves and the stems, and the
reproductive parts of the plant, which include flowers and fruits. The shoot
system generally grows above ground, where it absorbs the light needed for
photosynthesis. The root system, which supports the plants and absorbs
water and minerals, is usually underground. [link] shows the organ systems
of a typical plant.
Reproductive
Vegetative
Shoot system
Root system
The shoot system of a plant
consists of leaves, stems, flowers,
and fruits. The root system
anchors the plant while absorbing
water and minerals from the soil.
Plant Tissues
Plants are multicellular eukaryotes with tissue systems made of various cell
types that carry out specific functions. Plant tissue systems fall into one of
two general types: meristematic tissue, and permanent (or non-
meristematic) tissue. Cells of the meristematic tissue are found in
meristems, which are plant regions of continuous cell division and growth.
Meristematic tissue cells are either undifferentiated or incompletely
differentiated, and they continue to divide and contribute to the growth of
the plant. In contrast, permanent tissue consists of plant cells that are no
longer actively dividing.
Meristematic tissues consist of three types, based on their location in the
plant. Apical meristems contain meristematic tissue located at the tips of
stems and roots, which enable a plant to extend in length. Lateral
meristems facilitate growth in thickness or girth in a maturing plant.
Intercalary meristems occur only in monocots, at the bases of leaf blades
and at nodes (the areas where leaves attach to a stem). This tissue enables
the monocot leaf blade to increase in length from the leaf base; for example,
it allows lawn grass leaves to elongate even after repeated mowing.
Meristems produce cells that quickly differentiate, or specialize, and
become permanent tissue. Such cells take on specific roles and lose their
ability to divide further. They differentiate into three main types: dermal,
vascular, and ground tissue. Dermal tissue covers and protects the plant,
and vascular tissue transports water, minerals, and sugars to different parts
of the plant. Ground tissue serves as a site for photosynthesis, provides a
supporting matrix for the vascular tissue, and helps to store water and
sugars.
Secondary tissues are either simple (composed of similar cell types) or
complex (composed of different cell types). Dermal tissue, for example, is a
simple tissue that covers the outer surface of the plant and controls gas
exchange. Vascular tissue is an example of a complex tissue, and is made of
two specialized conducting tissues: xylem and phloem. Xylem tissue
transports water and nutrients from the roots to different parts of the plant,
and includes three different cell types: vessel elements and tracheids (both
of which conduct water), and xylem parenchyma. Phloem tissue, which
transports organic compounds from the site of photosynthesis to other parts
of the plant, consists of four different cell types: sieve cells (which conduct
photosynthates), companion cells, phloem parenchyma, and phloem fibers.
Unlike xylem conducting cells, phloem conducting cells are alive at
maturity. The xylem and phloem always lie adjacent to each other ({link]).
In stems, the xylem and the phloem form a structure called a vascular
bundle; in roots, this is termed the vascular cylinder.
200 ym
This light micrograph shows a cross
section of a squash (Curcurbita maxima)
stem. Each teardrop-shaped vascular
bundle consists of large xylem vessels
toward the inside and smaller phloem
cells toward the outside. Xylem cells,
which transport water and nutrients from
the roots to the rest of the plant, are dead
at functional maturity. Phloem cells,
which transport sugars and other organic
compounds from photosynthetic tissue to
the rest of the plant, are living. The
vascular bundles are encased in ground
tissue and surrounded by dermal tissue.
(credit: modification of work by "
(biophotos)"/Flickr; scale-bar data from
Matt Russell)
Stems
Stems are a part of the shoot system of a plant. They may range in length
from a few millimeters to hundreds of meters, and also vary in diameter,
depending on the plant type. Stems are usually above ground, although the
stems of some plants, such as the potato, also grow underground. Stems
may be herbaceous (soft) or woody in nature. Their main function is to
provide support to the plant, holding leaves, flowers and buds; in some
cases, stems also store food for the plant. A stem may be unbranched, like
that of a palm tree, or it may be highly branched, like that of an oak or pine
tree. The stem of the plant connects the roots to the leaves, helping to
transport absorbed water and minerals to different parts of the plant. It also
helps to transport the products of photosynthesis, namely sugars, from the
leaves to the rest of the plant.
Plant stems, whether above or below ground, are characterized by the
presence of nodes and internodes ([link]). Nodes are points of attachment
for leaves, aerial roots, and flowers. The stem region between two nodes is
called an internode. The stalk that extends from the stem to the base of the
leaf is the petiole. An axillary bud is usually found in the axil—the area
between the base of a leaf and the stem—where it can give rise to a branch
or a flower. The apex (tip) of the shoot contains the apical meristem within
the apical bud.
Internode
Petiole
Leaves are attached to the plant
stem at areas called nodes. An
internode is the stem region
between two nodes. The petiole is
the stalk connecting the leaf to the
stem. The leaves just above the
nodes arose from axillary buds.
Stem Anatomy
The stem and other plant organs arise from the ground tissue, and are
primarily made up of simple tissues formed from three types of cells:
parenchyma, collenchyma, and sclerenchyma cells.
Parenchyma cells are the most common plant cells ([link]). They are found
in the stem, the root, the inside of the leaf, and the pulp of the fruit.
Parenchyma cells are responsible for metabolic functions, such as
photosynthesis, and they help repair and heal wounds. Some parenchyma
cells also store starch.
The stem of common St John's
Wort (Hypericum perforatum) is
shown in cross section in this light
micrograph. The central pith
(greenish-blue, in the center) and
peripheral cortex (narrow zone 3—
5 cells thick just inside the
epidermis) are composed of
parenchyma cells. Vascular tissue
composed of xylem (red) and
phloem tissue (green, between the
xylem and cortex) surrounds the
pith. (credit: Rolf-Dieter Mueller)
Collenchyma cells are elongated cells with unevenly thickened walls
({link]). They provide structural support, mainly to the stem and leaves.
These cells are alive at maturity and are usually found below the epidermis.
The “strings” of a celery stalk are an example of collenchyma cells.
4
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i) ( Ss)
ik 14 @
Collenchyma cell walls are uneven
in thickness, as seen in this light
micrograph. They provide support
to plant structures. (credit:
modification of work by Carl
Szczerski; scale-bar data from
Matt Russell)
Sclerenchyma cells also provide support to the plant, but unlike
collenchyma cells, many of them are dead at maturity. There are two types
of sclerenchyma cells: fibers and sclereids. Both types have secondary cell
walls that are thickened with deposits of lignin, an organic compound that is
a key component of wood. Fibers are long, slender cells; sclereids are
smaller-sized. Sclereids give pears their gritty texture. Humans use
sclerenchyma fibers to make linen and rope ([link]).
Phloem
Epidermis Cortex Sclerenchyma
(a)
The central pith and outer cortex of the (a) flax
stem are made up of parenchyma cells. Inside the
cortex is a layer of sclerenchyma cells, which
make up the fibers in flax rope and clothing.
Humans have grown and harvested flax for
thousands of years. In (b) this drawing, fourteenth-
century women prepare linen. The (c) flax plant is
grown and harvested for its fibers, which are used
to weave linen, and for its seeds, which are the
source of linseed oil. (credit a: modification of
work by Emmanuel Boutet based on original work
by Ryan R. MacKenzie; credit c: modification of
work by Brian Dearth; scale-bar data from Matt
Russell)
Like the rest of the plant, the stem has three tissue systems: dermal,
vascular, and ground tissue. Each is distinguished by characteristic cell
types that perform specific tasks necessary for the plant’s growth and
survival.
Dermal Tissue
The dermal tissue of the stem consists primarily of epidermis, a single layer
of cells covering and protecting the underlying tissue. Woody plants have a
tough, waterproof outer layer of cork cells commonly known as bark, which
further protects the plant from damage. Epidermal cells are the most
numerous and least differentiated of the cells in the epidermis. The
epidermis of a leaf also contains openings known as stomata, through which
the exchange of gases takes place ([{link]). Two cells, known as guard cells,
surround each leaf stoma, controlling its opening and closing and thus
regulating the uptake of carbon dioxide and the release of oxygen and water
vapor. Trichomes are hair-like structures on the epidermal surface. They
help to reduce transpiration (the loss of water by aboveground plant parts),
increase solar reflectance, and store compounds that defend the leaves
against predation by herbivores.
Guard cells Open stoma Closed stoma
(b)
L> Guard cells
Stomatal pore
= Epidermal cells
Openings called stomata (singular: stoma) allow a plant to take
up carbon dioxide and release oxygen and water vapor. The (a)
colorized scanning-electron micrograph shows a closed stoma
of a eudicot. Each stoma is flanked by two guard cells that
regulate its (b) opening and closing. The (c) guard cells sit
within the layer of epidermal cells (credit a: modification of
work by Louisa Howard, Rippel Electron Microscope Facility,
Dartmouth College; credit b: modification of work by June
Kwak, University of Maryland; scale-bar data from Matt
Russell)
Vascular Tissue
The xylem and phloem that make up the vascular tissue of the stem are
arranged in distinct strands called vascular bundles, which run up and down
the length of the stem. When the stem is viewed in cross section, the
vascular bundles of eudicot stems are arranged in a ring. In plants with
stems that live for more than one year, the individual bundles grow together
and produce the characteristic growth rings. In monocot stems, the vascular
bundles are randomly scattered throughout the ground tissue ([Link]).
Eudicot stem Monocot stem
In (a) eudicot stems, vascular bundles are arranged
around the periphery of the ground tissue. The
xylem tissue is located toward the interior of the
vascular bundle, and phloem is located toward the
exterior. Sclerenchyma fibers cap the vascular
bundles. In (b) monocot stems, vascular bundles
composed of xylem and phloem tissues are
scattered throughout the ground tissue.
Xylem tissue has three types of cells: xylem parenchyma, tracheids, and
vessel elements. The latter two types conduct water and are dead at
maturity. Tracheids are xylem cells with thick secondary cell walls that are
lignified. Water moves from one tracheid to another through regions on the
side walls known as pits, where secondary walls are absent. Vessel elements
are xylem cells with thinner walls; they are shorter than tracheids. Each
vessel element is connected to the next by means of a perforation plate at
the end walls of the element. Water moves through the perforation plates to
travel up the plant.
Phloem tissue is composed of sieve-tube cells, companion cells, phloem
parenchyma, and phloem fibers. A series of sieve-tube cells (also called
sieve-tube elements) are arranged end to end to make up a long sieve tube,
which transports organic substances such as sugars and amino acids. The
sugars flow from one sieve-tube cell to the next through perforated sieve
plates, which are found at the end junctions between two cells. Although
still alive at maturity, the nucleus and other cell components of the sieve-
tube cells have disintegrated. Companion cells are found alongside the
sieve-tube cells, providing them with metabolic support. The companion
cells contain more ribosomes and mitochondria than the sieve-tube cells,
which lack some cellular organelles.
Ground Tissue
Ground tissue is mostly made up of parenchyma cells, but may also contain
collenchyma and sclerenchyma cells that help support the stem. The ground
tissue towards the interior of the vascular tissue in a stem or root is known
as pith, while the layer of tissue between the vascular tissue and the
epidermis is known as the cortex.
Growth in Stems
Growth in plants occurs as the stems and roots lengthen. Some plants,
especially those that are woody, also increase in thickness during their life
span. The increase in length of the shoot and the root is referred to as
primary growth, and is the result of cell division in the shoot apical
meristem. Secondary growth is characterized by an increase in thickness
or girth of the plant, and is caused by cell division in the lateral meristem.
[link] shows the areas of primary and secondary growth in a plant.
Herbaceous plants mostly undergo primary growth, with hardly any
secondary growth or increase in thickness. Secondary growth or “wood” is
noticeable in woody plants; it occurs in some eudicots, but occurs very
rarely in monocots.
Primary growth Secondary growth
Primary
Secondary Cork
phloem phloem
Pith
~ / Cortex
Vascular
cambium
Phloem Sclerenchyma
F Epidermis
Xylem Primary
xylem Cork
Secondary cambium
xylem
In woody plants, primary growth is followed by
secondary growth, which allows the plant stem to
increase in thickness or girth. Secondary vascular
tissue is added as the plant grows, as well as a cork
layer. The bark of a tree extends from the vascular
cambium to the epidermis.
Some plant parts, such as stems and roots, continue to grow throughout a
plant’s life: a phenomenon called indeterminate growth. Other plant parts,
such as leaves and flowers, exhibit determinate growth, which ceases when
a plant part reaches a particular size.
Annual Rings
The activity of the vascular cambium gives rise to annual growth rings.
During the spring growing season, cells of the secondary xylem have a
large internal diameter and their primary cell walls are not extensively
thickened. This is known as early wood, or spring wood. During the fall
season, the secondary xylem develops thickened cell walls, forming late
wood, or autumn wood, which is denser than early wood. This alternation
of early and late wood is due largely to a seasonal decrease in the number of
vessel elements and a seasonal increase in the number of tracheids. It results
in the formation of an annual ring, which can be seen as a circular ring in
the cross section of the stem ({link]). An examination of the number of
annual rings and their nature (such as their size and cell wall thickness) can
reveal the age of the tree and the prevailing climatic conditions during each
season.
The rate of wood growth increases
in summer and decreases in winter,
producing a characteristic ring for
each year of growth. Seasonal
changes in weather patterns can
also affect the growth rate—note
how the rings vary in thickness.
(credit: Adrian Pingstone)
Roots
The roots of seed plants have three major functions: anchoring the plant to
the soil, absorbing water and minerals and transporting them upwards, and
storing the products of photosynthesis. Some roots are modified to absorb
moisture and exchange gases. Most roots are underground. Some plants,
however, also have adventitious roots, which emerge above the ground
from the shoot.
Types of Root Systems
Root systems are mainly of two types ([link]). Eudicots have a tap root
system, while monocots have a fibrous root system. A tap root system has
a main root that grows down vertically, and from which many smaller
lateral roots arise. Dandelions are a good example; their tap roots usually
break off when trying to pull these weeds, and they can regrow another
shoot from the remaining root). A tap root system penetrates deep into the
soil. In contrast, a fibrous root system is located closer to the soil surface,
and forms a dense network of roots that also helps prevent soil erosion
(lawn grasses are a good example, as are wheat, rice, and corn). Some
plants have a combination of tap roots and fibrous roots. Plants that grow in
dry areas often have deep root systems, whereas plants growing in areas
with abundant water are likely to have shallower root systems.
(a) Taproot system (b) Fibrous root system
(a) Tap root systems have a main root that
grows down, while (b) fibrous root systems
consist of many small roots. (credit b:
modification of work by “Austen
Squarepants”/Flickr)
Leaves
Leaves are the main sites for photosynthesis: the process by which plants
synthesize food. Most leaves are usually green, due to the presence of
chlorophyll in the leaf cells. However, some leaves may have different
colors, caused by other plant pigments that mask the green chlorophyll.
The thickness, shape, and size of leaves are adapted to the environment.
Each variation helps a plant species maximize its chances of survival in a
particular habitat. Usually, the leaves of plants growing in tropical
rainforests have larger surface areas than those of plants growing in deserts
or very cold conditions, which are likely to have a smaller surface area to
minimize water loss.
Structure of a Typical Leaf
Each leaf typically has a leaf blade called the lamina, which is also the
widest part of the leaf. Some leaves are attached to the plant stem by a
petiole. Leaves that do not have a petiole and are directly attached to the
plant stem are called sessile leaves. Small green appendages usually found
at the base of the petiole are known as stipules. Most leaves have a midrib,
which travels the length of the leaf and branches to each side to produce
veins of vascular tissue. The edge of the leaf is called the margin. [link]
shows the structure of a typical eudicot leaf.
Deceptively simple in appearance,
a leaf is a highly efficient
structure.
Within each leaf, the vascular tissue forms veins. The arrangement of veins
in a leaf is called the venation pattern. Monocots and eudicots differ in their
patterns of venation ({link]). Monocots have parallel venation; the veins run
in straight lines across the length of the leaf without converging at a point.
In eudicots, however, the veins of the leaf have a net-like appearance,
forming a pattern known as reticulate venation. One extant plant, the
Ginkgo biloba, has dichotomous venation where the veins fork.
(a) (b) (c)
(a) Tulip (Tulipa), a monocot, has leaves with
parallel venation. The netlike venation in this (b)
linden (Tilia cordata) leaf distinguishes it as a
eudicot. The (c) Ginkgo biloba tree has dichotomous
venation. (credit a photo: modification of work by
“Drewboy64”/Wikimedia Commons; credit b photo:
modification of work by Roger Griffith; credit c
photo: modification of work by
"geishaboy500"/Flickr; credit abc illustrations:
modification of work by Agnieszka Kwiecien)
Plant Sensory Systems and Responses
Introduction
"Plants are extraordinary. For instance ... if you pinch a leaf of a plant you
set off electrical impulse. You can't touch a plant without setting off an
electrical impulse ... There is no question that plants have all kinds of
sensitivities. They do a lot of responding to an environment. They can do
almost anything you can think of. " Barbara McClintock, Nobel prize-
winning geneticist, in George Ritzer and Barry Smart, Handbook of Social
Theory (2001)
Animals can respond to environmental factors by moving to a new location.
Plants, however, are rooted in place and must respond to the surrounding
environmental factors. Plants have sophisticated systems to detect and
respond to light, gravity, temperature, and physical touch. Receptors sense
environmental factors and relay the information to effector systems—often
through intermediate chemical messengers—to bring about plant responses.
Plant Responses to Light
Plants have a number of sophisticated uses for light that go far beyond their
ability to photosynthesize low-molecular-weight sugars using only carbon
dioxide, light, and water. Photomorphogenesis is the growth and
development of plants in response to light. It allows plants to optimize their
use of light and space. Photoperiodism is the ability to use light to track
time. Plants can tell the time of day and time of year by sensing and using
various wavelengths of sunlight. Phototropism is a directional response
that allows plants to grow towards, or even away from, light.
The sensing of light in the environment is important to plants; it can be
crucial for competition and survival. The response of plants to light is
mediated by different photoreceptors, which are comprised of a protein
covalently bonded to a light-absorbing pigment called a chromophore.
Together, the two are called a chromoprotein.
Phototropism
Phototropism—the directional bending of a plant toward or away from a
light source—is a response to blue wavelengths of light. Positive
phototropism is growth towards a light source ({link]), while negative
phototropism is growth away from light.
In their 1880 treatise The Power of Movements in Plants, Charles Darwin
and his son Francis first described phototropism as the bending of seedlings
toward light. Darwin observed that light was perceived by the tip of the
plant (the apical meristem), but that the response (bending) took place in a
different part of the plant. They concluded that the signal had to travel from
the apical meristem to the base of the plant.
Sunflowers in a field near Hutchinson, KS display a
phototropic response by bending toward the light.
(credit: David A. Rintoul)
In 1913, Peter Boysen-Jensen demonstrated that a chemical signal produced
in the plant tip was responsible for the bending at the base. He cut off the
tip of a seedling, covered the cut section with a layer of gelatin, and then
replaced the tip. The seedling bent toward the light when illuminated.
However, when impermeable mica flakes were inserted between the tip and
the cut base, the seedling did not bend. A refinement of the experiment
showed that the signal traveled on the shaded side of the seedling. When the
mica plate was inserted on the illuminated side, the plant did bend towards
the light. Therefore, the chemical signal was a growth stimulant because the
phototropic response involved faster cell elongation on the shaded side than
on the illuminated side. We now know that the plant hormone auxin
influences plant stem cell elongation, and accumulates on the shaded side of
stems.
Plant Responses to Gravity
Whether or not they germinate in the light or in total darkness, shoots
usually sprout up from the ground, and roots grow downward into the
ground. A plant laid on its side in the dark will send shoots upward when
given enough time. Gravitropism ensures that roots grow into the soil and
that shoots grow toward sunlight. Growth of the shoot apical tip upward is
called negative gravitropism, whereas growth of the roots downward is
called positive gravitropism.
Amyloplasts (also known as statoliths) are specialized plastids that contain
starch granules and settle downward in response to gravity. Amyloplasts are
found in shoots and in specialized cells of the root cap. When a plant is
tilted, the statoliths drop to the new bottom cell wall. A few hours later, the
shoot or root will show growth in the new vertical direction.
The mechanism that mediates gravitropism is reasonably well understood.
When amyloplasts settle to the bottom of the gravity-sensing cells in the
root or shoot, they physically contact the endoplasmic reticulum (ER),
causing the release of calcium ions from inside the ER. This calcium
signaling in the cells causes polar transport of the plant hormone auxin to
the bottom of the cell. In roots, a high concentration of auxin inhibits cell
elongation. The effect slows growth on the lower side of the root, while
cells develop normally on the upper side. Auxin has the opposite effect in
shoots, where a higher concentration at the lower side of the shoot
stimulates cell expansion, causing the shoot to grow up. After the shoot or
root begin to grow vertically, the amyloplasts return to their normal
position. Other hypotheses—involving the entire cell in the gravitropism
effect—have been proposed to explain why some mutants that lack
amyloplasts may still exhibit a weak gravitropic response.
Growth Responses
A plant’s sensory response to external stimuli relies on chemical
messengers (hormones). Plant hormones affect all aspects of plant life, from
flowering to fruit setting and maturation, and from phototropism to leaf fall.
Potentially every cell in a plant can produce plant hormones. They can act
in their cell of origin or be transported to other portions of the plant body,
with many plant responses involving the synergistic or antagonistic
interaction of two or more hormones. In contrast, animal hormones are
produced in specific glands and transported to a distant site for action, and
they act alone.
Plant hormones are a group of unrelated chemical substances that affect
plant morphogenesis. Five major plant hormones are traditionally
described: auxins, cytokinins, gibberellins, ethylene, and abscisic acid. In
addition, other nutrients and environmental conditions can be characterized
as growth factors.
Auxins
The term auxin is derived from the Greek word auxein, which means "to
grow.” Auxins are the main hormones responsible for cell elongation in
phototropism and gravitropism. They also control the differentiation of
meristem into vascular tissue, and promote leaf development and
arrangement. While many synthetic auxins are used as herbicides, IAA (a
type of auxin) is the only naturally occurring auxin that shows physiological
activity. Apical dominance—the inhibition of lateral bud formation—is
triggered by auxins produced in the apical meristem. Flowering, fruit
setting and ripening, and inhibition of abscission (leaf falling) are other
plant responses under the direct or indirect control of auxins. Auxins also
act as a relay for the effects of the blue light and red/far-red responses.
Commercial use of auxins is widespread in plant nurseries and for crop
production. IAA is used as a rooting hormone to promote growth of
adventitious roots on cuttings and detached leaves. Applying synthetic
auxins to tomato plants in greenhouses promotes normal fruit development.
Outdoor application of auxin promotes synchronization of fruit setting and
dropping to coordinate the harvesting season. Fruits such as seedless
cucumbers can be induced to set fruit by treating unfertilized plant flowers
with auxins.
Cytokinins
The effect of cytokinins was first reported when it was found that adding
the liquid endosperm of coconuts to developing plant embryos in culture
stimulated their growth. The stimulating growth factor was found to be
cytokinin, a hormone that promotes cytokinesis (cell division). Almost 200
naturally occurring or synthetic cytokinins are known to date. Cytokinins
are most abundant in growing tissues, such as roots, embryos, and fruits,
where cell division is occurring. Cytokinins are known to delay senescence
in leaf tissues, promote mitosis, and stimulate differentiation of the
meristem in shoots and roots. Many effects on plant development are under
the influence of cytokinins, either in conjunction with auxin or another
hormone. For example, apical dominance seems to result from a balance
between auxins that inhibit lateral buds, and cytokinins that promote
bushier growth.
Gibberellins
Gibberellins (GAs) are a group of about 125 closely related plant
hormones that stimulate shoot elongation, seed germination, and fruit and
flower maturation. GAs are synthesized in the root and stem apical
meristems, young leaves, and seed embryos. In urban areas, GA antagonists
are sometimes applied to trees under power lines to control growth and
reduce the frequency of pruning.
GAs break dormancy (a state of inhibited growth and development) in the
seeds of plants that require exposure to cold or light to germinate. Abscisic
acid is a strong antagonist of GA action. Other effects of GAs include
gender expression, seedless fruit development, and the delay of senescence
in leaves and fruit. Seedless grapes are obtained through standard breeding
methods and contain inconspicuous seeds that fail to develop. Because GAs
are produced by the seeds, and because fruit development and stem
elongation are under GA control, these varieties of grapes would normally
produce small fruit in compact clusters. Maturing grapes are routinely
treated with GA to promote larger fruit size, as well as looser bunches
(longer stems), which reduces the instance of mildew infection ([Link]).
In grapes, application of
gibberellic acid increases
the size of fruit and
loosens clustering.
(credit: Bob Nichols,
USDA)
Abscisic Acid
The plant hormone abscisic acid (ABA) was first discovered as the agent
that causes the abscission or dropping of cotton bolls. However, more recent
studies indicate that ABA plays only a minor role in the abscission process.
ABA accumulates as a response to stressful environmental conditions, such
as dehydration, cold temperatures, or shortened day lengths. Its activity
counters many of the growth-promoting effects of GAs and auxins. ABA
inhibits stem elongation and induces dormancy in lateral buds.
ABA induces dormancy in seeds by blocking germination and promoting
the synthesis of storage proteins. Plants adapted to temperate climates
require a long period of cold temperature before seeds germinate. This
mechanism protects young plants from sprouting too early during
unseasonably warm weather in winter. As the hormone gradually breaks
down over winter, the seed is released from dormancy and germinates when
conditions are favorable in spring. Another effect of ABA is to promote the
development of winter buds; it mediates the conversion of the apical
meristem into a dormant bud. Low soil moisture causes an increase in
ABA, which causes stomata to close, reducing water loss in winter buds.
Ethylene
Ethylene is associated with fruit ripening, flower wilting, and leaf fall.
Ethylene is unusual because it is a volatile gas (C)H,). Hundreds of years
ago, when gas street lamps were installed in city streets, trees that grew
close to lamp posts developed twisted, thickened trunks and shed their
leaves earlier than expected. These effects were caused by ethylene
volatilizing from the lamps.
Aging tissues (especially senescing leaves) and nodes of stems produce
ethylene. The best-known effect of the hormone, however, is the promotion
of fruit ripening. Ethylene stimulates the conversion of starch and acids to
sugars. Some people store unripe fruit, such as avocadoes, in a sealed paper
bag to accelerate ripening; the gas released by the first fruit to mature will
speed up the maturation of the remaining fruit. Ethylene also triggers leaf
and fruit abscission, flower fading and dropping, and promotes germination
in some cereals and sprouting of bulbs and potatoes.
Ethylene is widely used in agriculture. Commercial fruit growers control
the timing of fruit ripening with application of the gas. Horticulturalists
inhibit leaf dropping in ornamental plants by removing ethylene from
greenhouses using fans and ventilation.
Plant Responses to Wind and Touch
The shoot of a pea plant winds around a trellis, while a tree grows on an
angle in response to strong prevailing winds. These are examples of how
plants respond to touch or wind.
The movement of a plant subjected to constant directional pressure is called
thigmotropism, from the Greek words thigma meaning “touch,” and
tropism implying “direction.” Tendrils are one example of this. The
meristematic region of tendrils is very touch sensitive; light touch will
evoke a quick coiling response. Cells in contact with a support surface
contract, whereas cells on the opposite side of the support expand.
Application of jasmonic acid is sufficient to trigger tendril coiling without a
mechanical stimulus.
A thigmonastic response is a touch response independent of the direction of
stimulus. In the Venus flytrap, two modified leaves are joined at a hinge and
lined with thin fork-like tines along the outer edges. Tiny hairs are located
inside the trap. When an insect brushes against these trigger hairs, touching
two or more of them in succession, the leaves close quickly, trapping the
prey. Glands on the leaf surface secrete enzymes that slowly digest the
insect. The released nutrients are absorbed by the leaves, which reopen for
the next meal.
Thigmomorphogenesis is a slow developmental change in the shape of a
plant subjected to continuous mechanical stress. When trees bend in the
wind, for example, growth is usually stunted and the trunk thickens.
Strengthening tissue, especially xylem, is produced to add stiffness to resist
the wind’s force. Researchers hypothesize that mechanical strain induces
growth and differentiation to strengthen the tissues. Ethylene and jasmonate
are likely involved in thigmomorphogenesis.
Reproductive Development and Structure
Introduction
"Flowers are the sweetest things that God ever made, and forgot to put a
soul into." Henry Ward Beecher, in Proverbs from Plymouth Pulpit (1887)
Flowers have fascinated humans for millenia, with their marvelous shapes
and enticing aromas. But the plant has another goal in mind besides
pleasing the human eye and nose, and that is reproduction. Sexual
reproduction takes place with slight variations in different groups of plants.
Plants have two distinct stages in their lifecycle: the gametophyte stage and
the sporophyte stage. The haploid gametophyte produces the male and
female gametes by mitosis in distinct multicellular structures. Fusion of the
male and females gametes forms the diploid zygote, which develops into
the sporophyte. After reaching maturity, the diploid sporophyte produces
spores by meiosis, which in turn divide by mitosis to produce the haploid
gametophyte. The new gametophyte produces gametes, and the cycle
continues. This is the alternation of generations, and is typical of plant
reproduction ([link]).
Angiosperm Life Cycle
Flower
Zygote within
parent ovary a
Independent
Sporophyte
Embryo within Mitosis
ee
Mitosis
Diploid (2N)
The angiosperm life cycle with alternation of generations is depicted in
this diagram. Work by Robert A. Bear and Eva Horne
The life cycle of higher plants is dominated by the sporophyte stage, with
the gametophyte borne on the sporophyte. In ferns, the gametophyte is free-
living and very distinct in structure from the diploid sporophyte. In
bryophytes, such as mosses, the haploid gametophyte is more developed
than the sporophyte.
During the vegetative phase of growth, plants increase in size and produce a
shoot system and a root system. As they enter the reproductive phase, some
of the branches start to bear flowers. Many flowers are borne singly,
whereas some are borne in clusters. The flower is borne on a stalk known as
a receptacle. Flower shape, color, and size are unique to each species, and
are often used by taxonomists to classify plants.
Sexual Reproduction in Angiosperms
The lifecycle of angiosperms follows the alternation of generations
explained previously. The haploid gametophyte alternates with the diploid
sporophyte during the sexual reproduction process of angiosperms. Flowers
contain the plant’s reproductive structures.
Flower Structure
A typical flower has four main parts—or whorls—known as the calyx,
corolla, androecium, and gynoecium ([link]). The outermost whorl of the
flower has green, leafy structures known as sepals. The sepals, collectively
called the calyx, help to protect the unopened bud. The second whorl is
comprised of petals—usually, brightly colored—collectively called the
corolla. The number of sepals and petals varies depending on whether the
plant is a monocot or eudicot. In monocots, petals usually number three or
multiples of three; in eudicots, the number of petals is four or five, or
multiples of four and five. Together, the calyx and corolla are known as the
perianth. The third whorl contains the male reproductive structures and is
known as the androecium. The androecium has stamens with anthers that
contain the microsporangia. The innermost group of structures in the flower
is the gynoecium, or the female reproductive component(s). The carpel is
the individual unit of the gynoecium and has a stigma, style, and ovary. A
flower may have one or multiple carpels.
Stamens
Petal
Flower
Corolla (composed of petals)
Calyx (composed of sepals)
The four main parts of the flower are the calyx, corolla, androecium,
and gynoecium. The androecium is the sum of all the male
reproductive organs, and the gynoecium is the sum of the female
reproductive organs. (credit: modification of work by Mariana Ruiz
Villareal)
If the anther is missing, what type of reproductive structure will the flower
be unable to produce? What term is used to describe an incomplete flower
lacking the androecium? What term describes an incomplete flower lacking
a gynoecium?
If all four whorls (the calyx, corolla, androecium, and gynoecium) are
present, the flower is described as complete. If any of the four parts is
missing, the flower is known as incomplete. Flowers that contain both an
androecium and a gynoecium are called perfect, androgynous or
hermaphrodites. There are two types of incomplete flowers: staminate
flowers contain only an androecium, and carpellate flowers have only a
gynoecium ([link]).
Staminate Carpellate
flowers flowers
Stem Corn Silk Ovary
and root kernels —_ (stigma)
The corn plant has both staminate
(male) and carpellate (female)
flowers. Staminate flowers, which
are clustered in the tassel at the tip
of the stem, produce pollen grains.
Carpellate flower are clustered in
the immature ears. Each strand of
silk is a stigma. The corn kernels
are seeds that develop on the ear
after fertilization. Also shown is
the lower stem and root.
If both male and female flowers are borne on the same plant, the species is
called monoecious (meaning “one home”): examples are corn and pea.
Species with male and female flowers borne on separate plants are termed
dioecious, or “two homes,” examples of which are C. papaya and
Cannabis. The ovary, which may contain one or multiple ovules, may be
placed above other flower parts, which is referred to as superior; or, it may
be placed below the other flower parts, referred to as inferior ((link]).
Sepals
Ovaries
(a) Superior flower (b) Inferior flower
The (a) lily is a superior flower, which has the ovary
above the other flower parts. (b) Fuchsia is an inferior
flower, which has the ovary beneath other flower parts.
(credit a photo: modification of work by Benjamin
Zwittnig; credit b photo: modification of work by
"Koshy Koshy"/Flickr)
Male Gametophyte (The Pollen Grain)
The male gametophyte develops and reaches maturity in an immature
anther. In a plant’s male reproductive organs, development of pollen takes
place in a structure known as the microsporangium ([link]). The
microsporangia, which are usually bi-lobed, are pollen sacs in which the
microspores develop into pollen grains. These are found in the anther,
which is at the end of the stamen—the long filament that supports the
anther.
Se Vicrospore
} mother cells
Tapetum
Pollensacs —~
(microsporangia)
Shown is (a) a cross section of an anther at two
developmental stages. The immature anther
(top) contains four microsporangia, or pollen
sacs. Each microsporangium contains hundreds
of microspore mother cells that will each give
rise to four pollen grains. The tapetum supports
the development and maturation of the pollen
grains. Upon maturation of the pollen
(bottom), the pollen sac walls split open and
the pollen grains (male gametophytes) are
released. (b) In these scanning electron
micrographs, pollen sacs are ready to burst,
releasing their grains. (credit b: modification of
work by Robert R. Wise; scale-bar data from
Matt Russell)
Within the microsporangium, the microspore mother cell divides by meiosis
to give rise to four microspores, each of which will ultimately form a pollen
grain ([link]). An inner layer of cells, known as the tapetum, provides
nutrition to the developing microspores and contributes key components to
the pollen wall. Mature pollen grains contain two cells: a generative cell
and a pollen tube cell. The generative cell is contained within the larger
pollen tube cell. Upon germination, the tube cell forms the pollen tube
through which the generative cell migrates to enter the ovary. During its
transit inside the pollen tube, the generative cell divides to form two male
gametes (sperm cells). Upon maturity, the microsporangia burst, releasing
the pollen grains from the anther.
Microspore
mother cell
Pollen
tube cell
Mature
pollen
grains
nucleus
Pollen develops from the microspore
mother cells. The mature pollen grain is
composed of two cells: the pollen tube
cell and the generative cell, which is
inside the tube cell. The pollen grain has
two coverings: an inner layer (intine) and
an outer layer (exine). The inset scanning
electron micrograph shows Arabidopsis
lyrata pollen grains. (credit “pollen
micrograph”: modification of work by
Robert R. Wise; scale-bar data from Matt
Russell)
Each pollen grain has two coverings: the exine (thicker, outer layer) and the
intine ({link]). The exine contains sporopollenin, a complex waterproofing
substance supplied by the tapetal cells. Sporopollenin allows the pollen to
survive under unfavorable conditions and to be carried by wind, water, or
biological agents without undergoing damage.
Female Gametophyte (The Embryo Sac)
While the details may vary between species, the overall development of the
female gametophyte has two distinct phases. First, in the process of
megasporogenesis, a single cell in the diploid megasporangium—an area of
tissue in the ovules—undergoes meiosis to produce four megaspores, only
one of which survives. During the second phase, megagametogenesis, the
surviving haploid megaspore undergoes mitosis to produce an eight-
nucleate, seven-cell female gametophyte, also known as the
megagametophyte or embryo sac. Two of the nuclei—the polar nuclei—
move to the equator and fuse, forming a single, diploid central cell. This
central cell later fuses with a sperm to form the triploid endosperm. Three
nuclei position themselves on the end of the embryo sac opposite the
micropyle and develop into the antipodal cells, which later degenerate. The
nucleus closest to the micropyle becomes the female gamete, or egg cell,
and the two adjacent nuclei develop into synergid cells ({link]). The
synergids help guide the pollen tube for successful fertilization, after which
they disintegrate. Once fertilization is complete, the resulting diploid zygote
develops into the embryo, and the fertilized ovule forms the other tissues of
the seed.
A double-layered integument protects the megasporangium and, later, the
embryo sac. The integument will develop into the seed coat after
fertilization and protect the entire seed. The ovule wall will become part of
the fruit. The integuments, while protecting the megasporangium, do not
enclose it completely, but leave an opening called the micropyle. The
micropyle allows the pollen tube to enter the female gametophyte for
fertilization.
Embryo Sac
Chalazal end
Antipodals
Polar nuclei
Synergids
Central Egg cell
cell
Micropylar end
As shown in this diagram of
the embryo sac in
angiosperms, the ovule is
covered by integuments and
has an opening called a
micropyle. Inside the
embryo sac are three
antipodal cells, two
synergids, a central cell, and
the egg cell.
Pollination and Fertilization
Introduction
"Nature is full of by-ends. A moth feeds on a petal, in a moment the pollen
caught on its breast will be wedding this blossom to another in the next
county." George Iles, in Canadian Stories (1918)
In angiosperms, pollination is defined as the placement or transfer of
pollen from the anther to the stigma of the same flower or another flower. In
gymnosperms, pollination involves pollen transfer from the male cone to
the female cone. Upon transfer, the pollen germinates to form the pollen
tube and the sperm for fertilizing the egg. Pollination has been well studied
since the time of Gregor Mendel. Mendel successfully carried out self- as
well as cross-pollination in garden peas while studying how characteristics
were passed on from one generation to the next. Today’s crops are a result
of plant breeding, which employs artificial selection to produce the present-
day cultivars. A case in point is today's corn, which is a result of years of
breeding that started with its ancestor, teosinte. The teosinte that the ancient
Mayans originally began cultivating had tiny seeds—vastly different from
today’s relatively giant ears of corn. Interestingly, though these two plants
appear to be entirely different, the genetic difference between them is
miniscule.
Pollination takes two forms: self-pollination and cross-pollination. Self-
pollination occurs when the pollen from the anther is deposited on the
stigma of the same flower, or another flower on the same plant. Cross-
pollination is the transfer of pollen from the anther of one flower to the
stigma of another flower on a different individual of the same species. Self-
pollination occurs in flowers where the stamen and carpel mature at the
same time, and are positioned so that the pollen can land on the flower’s
stigma. This method of pollination does not require an investment from the
plant to provide nectar and pollen as food for pollinators.
Living species are adapted to ensure survival of their progeny; those that
fail become extinct. Genetic diversity is therefore required so that in
changing environmental or stress conditions, some of the progeny can
survive. Self-pollination leads to the production of plants with less genetic
diversity, since genetic material from the same plant is used to form both
gametes, and eventually, the zygote. In contrast, cross-pollination—or out-
crossing—leads to greater genetic diversity because the microgametophyte
and megagametophyte are derived from different plants.
Because cross-pollination allows for more genetic diversity, plants have
developed many ways to avoid self-pollination. In some species, the pollen
and the ovary mature at different times. These flowers make self-pollination
nearly impossible. By the time pollen matures and has been shed, the
stigma of this flower is mature and can only be pollinated by pollen from
another flower. Some flowers have developed physical features that prevent
self-pollination. The primrose is one such flower. Primroses have evolved
two flower types with differences in anther and stigma length: the pin-eyed
flower has anthers positioned at the pollen tube’s halfway point, and the
thrum-eyed flower’s stigma is likewise located at the halfway point. Insects
easily cross-pollinate while seeking the nectar at the bottom of the pollen
tube. This phenomenon is also known as heterostyly. Many plants, such as
cucumber, have male and female flowers located on different parts of the
plant, thus making self-pollination difficult. In yet other species, the male
and female flowers are borne on different plants (dioecious). All of these
are barriers to self-pollination; therefore, the plants depend on pollinators to
transfer pollen. The majority of pollinators are biotic agents such as insects
(like bees, flies, and butterflies), bats, birds, and other animals. Other plant
species are pollinated by abiotic agents, such as wind and water.
Pollination by Insects
Bees are perhaps the most important pollinator of many garden plants and
most commercial fruit trees ((link]). The most common species of bees are
bumblebees and honeybees. Since bees cannot see the color red, bee-
pollinated flowers usually have shades of blue, yellow, or other colors. Bees
collect energy-rich pollen or nectar for their survival and energy needs.
They visit flowers that are open during the day, are brightly colored, have a
strong aroma or scent, and have a tubular shape, typically with the presence
of a nectar guide. A nectar guide includes regions on the flower petals that
are visible only to bees, and not to humans; it helps to guide bees to the
center of the flower, thus making the pollination process more efficient. The
pollen sticks to the bees’ fuzzy hair, and when the bee visits another flower,
some of the pollen is transferred to the second flower. Recently, there have
been many reports about the declining population of honeybees. Many
flowers will remain unpollinated and not bear seed if honeybees disappear.
The impact on commercial fruit growers could be devastating.
Insects, such as bees, are
important agents of pollination.
(credit: photo by D. A. Rintoul)
Many flies are attracted to flowers that have a decaying smell or an odor of
rotting flesh. These flowers, which produce nectar, usually have dull colors,
such as brown or purple. They are found on the corpse flower or voodoo
lily (Amorphophallus), dragon arum (Dracunculus), and carrion flower
(Stapleia, Rafflesia). The nectar provides energy, whereas the pollen
provides protein. Wasps are also important insect pollinators, and pollinate
many species of figs.
Butterflies, such as the monarch, pollinate many garden flowers and
wildflowers, which usually occur in clusters. These flowers are brightly
colored, have a strong fragrance, are open during the day, and have nectar
guides to make access to nectar easier. The pollen is picked up and carried
on the butterfly’s limbs. Moths, on the other hand, pollinate flowers during
the late afternoon and night. The flowers pollinated by moths are pale or
white and are flat, enabling the moths to land. One well-studied example of
a moth-pollinated plant is the yucca plant, which is pollinated by the yucca
moth. The shape of the flower and moth have adapted in such a way as to
allow successful pollination. The moth deposits pollen on the sticky stigma
for fertilization to occur later. The female moth also deposits eggs into the
ovary. As the eggs develop into larvae, they obtain food from the flower
and developing seeds. Thus, both the insect and flower benefit from each
other in this symbiotic relationship. The corn earworm moth and Gaura
plant have a similar relationship ((link]).
A corn earworm sips nectar from a
night-blooming Gaura plant.
(credit: Juan Lopez, USDA ARS)
Pollination by Bats
In the tropics and deserts, bats are often the pollinators of nocturnal flowers
such as agave, guava, and morning glory. The flowers are usually large and
white or pale-colored; thus, they can be distinguished from the dark
surroundings at night. The flowers have a strong, fruity, or musky fragrance
and produce large amounts of nectar. They are naturally large and wide-
mouthed to accommodate the head of the bat. As the bats seek the nectar,
their faces and heads become covered with pollen, which is then transferred
to the next flower.
Pollination by Birds
Many species of small birds, such as hummingbirds and the Australasian
birds known as honeyeaters ([link]), are pollinators for a wide variety of
plants. Flowers visited by birds are usually sturdy and are oriented in such a
way as to allow the birds to stay near the flower without getting their wings
entangled in the nearby flowers. The flower typically has a curved, tubular
shape, which allows access for the bird’s beak. Brightly colored, odorless
flowers that are open during the day are pollinated by birds. As a bird seeks
energy-rich nectar, pollen is deposited on the bird’s head and neck and is
then transferred to the next flower it visits. Botanists have been known to
determine the range of extinct plants by collecting and identifying pollen
from 200-year-old bird specimens from the same site.
Hummingbirds (shown at left) have adaptations (long beaks, ability to
hover, etc.) that allow them to reach the nectar of certain tubular
flowers, but in the process they can collect pollen on their beaks or
heads and then transfer it to another flower. Other birds, like the Tui
(at right), a honeyeater found in New Zealand, also collect pollen on
their foreheads as they forage on nectar. (credit: photos by D. A.
Rintoul)
Pollination by Wind
Most species of conifers, and many angiosperms, such as grasses, maples
and oaks, are pollinated by wind. Pine cones are brown and unscented,
while the flowers of wind-pollinated angiosperm species are usually green,
small, may have small or no petals, and produce large amounts of pollen.
Unlike the typical insect-pollinated flowers, flowers adapted to pollination
by wind do not produce nectar or scent. In wind-pollinated species, the
microsporangia hang out of the flower, and, as the wind blows, the
lightweight pollen is carried with it ([link]). The flowers usually emerge
early in the spring, before the leaves, so that the leaves do not block the
movement of the wind. The pollen is deposited on the exposed feathery
stigma of the flower ((link]).
A person knocks pollen from a
pine tree.
These male (a) and female (b) catkins are from the goat
willow tree (Salix caprea). Note how both structures are
light and feathery to better disperse and catch the wind-
blown pollen.
Pollination by Water
Some weeds, such as Australian sea grass and pond weeds, are pollinated
by water. The pollen floats on water, and when it comes into contact with
the flower, it is deposited inside the flower.
Note:
Evolution Connection
Pollination by Deception
Orchids are highly valued flowers, with many rare varieties ([link]). They
grow in a range of specific habitats, mainly in the tropics of Asia, South
America, and Central America. At least 25,000 species of orchids have
been identified.
Certain orchids use food deception
or sexual deception to attract
pollinators. Shown here is a bee
orchid (Ophrys apifera). (credit:
David Evans)
Flowers often attract pollinators with food rewards, in the form of nectar.
However, some species of orchid are an exception to this standard: they
have evolved different ways to attract the desired pollinators. They use a
method known as food deception, in which bright colors and perfumes are
offered, but no food. Anacamptis morio, commonly known as the green-
winged orchid, bears bright purple flowers and emits a strong scent. The
bumblebee, its main pollinator, is attracted to the flower because of the
strong scent—which usually indicates food for a bee—and in the process,
picks up the pollen to be transported to another flower.
Other orchids use sexual deception. Chiloglottis trapeziformis emits a
compound that smells the same as the pheromone emitted by a female
wasp to attract male wasps. The male wasp is attracted to the scent, lands
on the orchid flower, and in the process, transfers pollen. Some orchids,
like the Australian hammer orchid, use scent as well as visual trickery in
yet another sexual deception strategy to attract wasps. The flower of this
orchid mimics the appearance of a female wasp and emits a pheromone.
The male wasp tries to mate with what appears to be a female wasp, and in
the process, picks up pollen, which it then transfers to the next counterfeit
mate.
Double Fertilization
After pollen is deposited on the stigma, it must germinate and grow through
the style to reach the ovule. The microspores, or the pollen, contain two
cells: the pollen tube cell and the generative cell. The pollen tube cell grows
into a pollen tube through which the generative cell travels. The
germination of the pollen tube requires water, oxygen, and certain chemical
signals. As it travels through the style to reach the embryo sac, the pollen
tube’s growth is supported by the tissues of the style. In the meantime, if the
generative cell has not already split into two cells, it now divides to form
two sperm cells. The pollen tube is guided by the chemicals secreted by the
synergids present in the embryo sac, and it enters the ovule sac through the
micropyle. Of the two sperm cells, one sperm fertilizes the egg cell,
forming a diploid zygote; the other sperm fuses with the two polar nuclei,
forming a triploid cell that develops into the endosperm. Together, these
two fertilization events in angiosperms are known as double fertilization
({link]). After fertilization is complete, no other sperm can enter. The
fertilized ovule forms the seed, whereas the tissues of the ovary become the
fruit, usually enveloping the seed.
Pollen grain
Micropyle
Egg
Stigma
9 Pollen tube
Polar
Sperm ;
nuclei
Style Synergids
Egg
_— _— Polar
nuclei
Ovules Sperm
Ovary nuclei
Antipodals
Embryo sac
The pollen grain adheres to The pollen tube cell grows The pollen tube penetrates One of the sperm fertilizes
the stigma, which contains into the style. The generative an opening in the ovule the egg to form the diploid
two cells: a generative cell Cell travels inside the pollen called a micropyle. zygote. The other sperm
and a tube cell. tube. It divides to form two fertilizes two polar nuclei to
sperm. form the triploid endosperm,
which will become a food
source for the growing
embryo.
In angiosperms, one sperm fertilizes the egg to form the 2n
zygote, and the other sperm fertilizes the central cell to form
the 3n endosperm. This is called a double fertilization.
After fertilization, the zygote divides to form two cells: the upper cell, or
terminal cell, and the lower, or basal, cell. The division of the basal cell
gives rise to the suspensor, which eventually makes connection with the
maternal tissue. The suspensor provides a route for nutrition to be
transported from the mother plant to the growing embryo. The terminal cell
also divides, giving rise to a globular-shaped proembryo ([link]a). In
eudicots, the developing embryo has a heart shape, due to the presence of
the two rudimentary cotyledons ([link]b). In non-endospermic eudicots,
such as Capsella bursa, the endosperm develops initially, but is then
digested, and the food reserves are moved into the two cotyledons. As the
embryo and cotyledons enlarge, they run out of room inside the developing
seed, and are forced to bend ([link]c). Ultimately, the embryo and
cotyledons fill the seed ([link]d), and the seed is ready for dispersal.
Embryonic development is suspended after some time, and growth is
resumed only when the seed germinates. The developing seedling will rely
on the food reserves stored in the cotyledons until the first set of leaves
begin photosynthesis.
Cotyledons
werent s5%s =
>
ee
~ = 2%
a a
Proembryo
Embryo
Suspensor
ao
Liess
Suspensor
Basal cell
Basal cell
Short meristem
Endosperm
Cotyledons
Seed coat
Embryonic
axis Cotyledons
Root meristem
Shown are the stages of embryo
development in the ovule of a shepherd’s
purse (Capsella bursa). After fertilization,
the zygote divides to form an upper terminal
cell and a lower basal cell. (a) In the first
stage of development, the terminal cell
divides, forming a globular pro-embryo. The
basal cell also divides, giving rise to the
suspensor. (b) In the second stage, the
developing embryo has a heart shape due to
the presence of cotyledons. (c) In the third
stage, the growing embryo runs out of room
and starts to bend. (d) Eventually, it
completely fills the seed. (credit:
modification of work by Robert R. Wise;
scale-bar data from Matt Russell)
Development of the Seed
The mature ovule develops into the seed. A typical seed contains a seed
coat, cotyledons, endosperm, and a single embryo ([link]).
Endosperm
Epicotyl
Hypocoty|
Radicle Embryo
Cotyledon
Seed coat
Bean seed Corn seed
(Eudicot) (Monocot)
The structures of eudicot and monocot seeds
are shown. Eudicots (left) have two
cotyledons. Monocots, such as corn (right),
have one cotyledon, called the scutellum; it
channels nutrition to the growing embryo.
Both monocot and eudicot embryos have a
plumule that forms the leaves, a hypocotyl
that forms the stem, and a radicle that forms
the root. The embryonic axis comprises
everything between the plumule and the
radicle, not including the cotyledon(s).
The storage of food reserves in angiosperm seeds differs between monocots
and eudicots. In monocots, such as corn and wheat, the single cotyledon is
connected directly to the embryo via vascular tissue (xylem and phloem).
Food reserves are stored in the large endosperm. Upon germination,
enzymes are secreted by the aleurone, a single layer of cells just inside the
seed coat that surrounds the endosperm and embryo. The enzymes degrade
the stored carbohydrates, proteins and lipids, the products of which are
absorbed by the cotyledon and transported to the developing embryo.
Therefore, the cotyledon can be seen to be an absorptive organ, not a
storage organ.
The two cotyledons in the eudicot seed also have vascular connections to
the embryo. In endospermic eudicots, the food reserves are stored in the
endosperm. During germination, the two cotyledons therefore act as
absorptive organs to take up the enzymatically released food reserves, much
like in monocots (monocots, by definition, also have endospermic seeds).
Tobacco (Nicotiana tabaccum), tomato (Solanum lycopersicum), and
pepper (Capsicum annuum) are examples of endospermic eudicots. In non-
endospermic eudicots, the triploid endosperm develops normally following
double fertilization, but the endosperm food reserves are quickly
remobilized and moved into the developing cotyledon for storage. The two
halves of a peanut seed (Arachis hypogaea) and the split peas (Pisum
sativum) of split pea soup are individual cotyledons loaded with food
reserves.
The seed, along with the ovule, is protected by a seed coat that is formed
from the integuments of the ovule sac. The embryo consists of three parts:
the plumule, the radicle, and the hypocotyl. The portion of the embryo
between the cotyledon attachment point and the radicle is known as the
hypocotyl (hypocotyl means “below the cotyledons”). The embryo
terminates in a radicle (the embryonic root), which is the region from
which the root will develop. In eudicots, the hypocotyls extend above
ground, giving rise to the stem of the plant. In monocots, the hypocotyl
does not show above ground because monocots do not exhibit stem
elongation. The part of the embryonic axis that projects above the
cotyledons is known as the epicotyl. The plumule is composed of the
epicotyl, young leaves, and the shoot apical meristem.
Upon germination in eudicot seeds ({link]), the epicotyl is shaped like a
hook with the plumule pointing downwards. This shape is called the
plumule hook, and it persists as long as germination proceeds in the dark.
Therefore, as the epicotyl pushes through the tough and abrasive soil, the
plumule is protected from damage. Upon exposure to light, the hypocotyl
hook straightens out, the young foliage leaves face the sun and expand, and
the epicotyl continues to elongate. During this time, the radicle is also
growing and producing the primary root. As it grows downward to form the
tap root, lateral roots branch off to all sides, producing the typical eudicot
tap root system.
Epicotyl
Hypoc otyl between cotyledons Cotyledo ns
Seed coat
J
a Seed coat
Radicle
Primary
Root
As this eudicot bean seed germinates, the primary root, or radicle,
emerges first, followed by the hypocotyl and cotyledons. Work by
Robert A. Bear
As a monocot seed germinates ([link]), the primary root emerges, protected
by the root-tip covering: the coleorhiza. Next, the primary shoot emerges,
protected by the coleoptile: the covering of the shoot tip. Upon exposure to
light (i.e. when the plumule has exited the soil and the protective coleoptile
is no longer needed), elongation of the coleoptile ceases and the leaves
expand and unfold. At the other end of the embryon, the primary root soon
dies, while other, adventitious roots (roots that do not arise from the usual
place — i.e. the root) emerge from the base of the stem. This gives the
monocot a fibrous root system.
Primary
root
Adventitious roots
As this monocot corn seed germinates, the primary root, or radicle,
emerges first, followed by the primary shoot, or coleoptile, and the
adventitious roots. Work by Robert A. Bear
Seed Germination
Many mature seeds enter a period of inactivity, or extremely low metabolic
activity: a process known as dormancy, which may last for months, years or
even centuries. Dormancy helps keep seeds viable during unfavorable
conditions. Upon a return to favorable conditions, seed germination takes
place. Favorable conditions could be as diverse as moisture, light, cold, fire,
or chemical treatments. After heavy rains, many new seedlings emerge.
Forest fires also lead to the emergence of new seedlings. Some seeds
require vernalization (cold treatment) before they can germinate. This
guarantees that seeds produced by plants in temperate climates will not
germinate until the spring. Plants growing in hot climates may have seeds
that need a heat treatment in order to germinate, to avoid germination in the
hot, dry summers. In many seeds, the presence of a thick seed coat retards
the ability to germinate. Scarification, which includes mechanical or
chemical processes to soften the seed coat, is often employed before
germination. Presoaking in hot water, or passing through an acid
environment, such as an animal’s digestive tract, may also be employed.
Depending on seed size, the time taken for a seedling to emerge may vary.
Species with large seeds have enough food reserves to germinate deep
below ground, and still extend their epicoty] all the way to the soil surface.
Seeds of small-seeded species usually require light as a germination cue.
This ensures the seeds only germinate at or near the soil surface (where the
light is greatest). If they were to germinate too far underneath the surface,
the developing seedling would not have enough food reserves to reach the
sunlight.
Development of Fruit and Fruit Types
After fertilization, the ovary of the flower usually develops into the fruit.
Fruits are usually associated with having a sweet taste; however, not all
fruits are sweet. Botanically, the term “fruit” is used for a ripened ovary. In
most cases, flowers in which fertilization has taken place will develop into
fruits, and flowers in which fertilization has not taken place will not. Some
fruits develop from the ovary and are known as true fruits, whereas others
develop from other parts of the female gametophyte and are known as
accessory fruits. The fruit encloses the seeds and the developing embryo,
thereby providing it with protection. Fruits are of many types, depending on
their origin and texture. The sweet tissue of the blackberry, the red flesh of
the tomato, the shell of the peanut, and the hull of corn (the tough, thin part
that gets stuck in your teeth when you eat popcorn) are all fruits. As the
fruit matures, the seeds also mature.
Fruits may be classified as simple, aggregate, multiple, or accessory,
depending on their origin ([link]). If the fruit develops from a single carpel
or fused carpels of a single ovary, it is known as a simple fruit, as seen in
nuts and beans. An aggregate fruit is one that develops from more than one
carpel, but all are in the same flower: the mature carpels fuse together to
form the entire fruit, as seen in the raspberry. Multiple fruit develops from
an inflorescence or a cluster of flowers. An example is the pineapple, where
the flowers fuse together to form the fruit. Accessory fruits (sometimes
called false fruits) are not derived from the ovary, but from another part of
the flower, such as the receptacle (strawberry) or the hypanthium (apples
and pears).
Simple fruit
Aggregate fruit
Multiple fruit
There are four main types of fruits. Simple
fruits, such as these nuts, are derived from a
single ovary. Aggregate fruits, like
raspberries, form from many carpels that
fuse together. Multiple fruits, such as
pineapple, form from a cluster of flowers
called an inflorescence. Accessory fruit, like
the apple, are formed from a part of the plant
other than the ovary. (credit "nuts":
modification of work by Petr Kratochvil;
credit "raspberries": modification of work
by Cory Zanker; credit "pineapple":
modification of work by Howie Le; credit
"apple": modification of work by Paolo
Neo)
Fruits generally have three parts: the exocarp (the outermost skin or
covering), the mesocarp (middle part of the fruit), and the endocarp (the
inner part of the fruit). Together, all three are known as the pericarp. The
mesocarp is usually the fleshy, edible part of the fruit; however, in some
fruits, such as the almond, the endocarp is the edible part. In many fruits,
two or all three of the layers are fused, and are indistinguishable at maturity.
Fruits can be dry or fleshy. Furthermore, fruits can be divided into dehiscent
or indehiscent types. Dehiscent fruits, such as peas, readily release their
seeds, while indehiscent fruits, like peaches, rely on decay to release their
seeds.
Fruit and Seed Dispersal
The fruit has a single purpose: seed dispersal. Seeds contained within fruits
need to be dispersed far from the mother plant, so they may find favorable
and less competitive conditions in which to germinate and grow.
Some fruit have built-in mechanisms so they can disperse by themselves,
whereas others require the help of agents like wind, water, and animals
({link]). Modifications in seed structure, composition, and size help in
dispersal. Wind-dispersed fruit are lightweight and may have wing-like
appendages that allow them to be carried by the wind. Some have a
parachute-like structure to keep them afloat. Some fruits—for example, the
dandelion—have hairy, nearly weightless structures that are suited to
dispersal by wind.
Seeds dispersed by water are contained in light and buoyant fruit, giving
them the ability to float. Coconuts are well known for their ability to float
on water to reach land where they can germinate. Similarly, willow and
silver birches produce lightweight fruit that can float on water.
Animals and birds eat fruits, and the seeds that are not digested are excreted
in their droppings some distance away. Some animals, like squirrels, bury
seed-containing fruits for later use; if the squirrel does not find its stash of
fruit, and if conditions are favorable, the seeds germinate. Some fruits, like
the cocklebur, have hooks or sticky structures that stick to an animal's coat
and are then transported to another place. Humans also play a big role in
dispersing seeds when they carry fruits to new places and throw away the
inedible part that contains the seeds.
All of the above mechanisms allow for seeds to be dispersed through space,
much like an animal’s offspring can move to a new location. Seed
dormancy, which was described earlier, allows plants to disperse their
progeny through time: something animals cannot do. Dormant seeds can
wait months, years, or even decades for the proper conditions for
germination and propagation of the species.
Fruits and seeds are dispersed by various
means. (a) Dandelion seeds are dispersed
by wind, the (b) coconut seed is dispersed
by water, and the (c) acorn is dispersed by
animals that cache and then forget it.
(credit a: modification of work by
"Rosendahl"/Flickr; credit b: modification
of work by Shine Oa; credit c:
modification of work by Paolo Neo)
Root and Leaf Structure
Introduction
"A tree nowhere offers a straight line or a regular curve, but who doubts
that root, trunk, boughs, and leaves embody geometry?" George Iles, in
Canadian Stories (1918)
We all recognize roots, trunks and leaves as parts of a plant. In this chapter
you will learn a bit more about those structures, and how they are parts of
plant organ systems.
Plant Organ Systems
In plants, just as in animals, similar cells working together form a tissue.
When different types of tissues work together to perform a unique function,
they form an organ; organs working together form organ systems. Vascular
plants have two distinct organ systems: a shoot system, and a root system.
The shoot system consists of two portions: the vegetative (non-
reproductive) parts of the plant, such as the leaves and the stems, and the
reproductive parts of the plant, which include flowers and fruits. The shoot
system generally grows above ground, where it absorbs the light needed for
photosynthesis. The root system, which supports the plants and absorbs
water and minerals, is usually underground. [link] shows the organ systems
of a typical plant.
Reproductive
Vegetative
Shoot system
Root system
The shoot system of a plant
consists of leaves, stems, flowers,
and fruits. The root system
anchors the plant while absorbing
water and minerals from the soil.
Roots
The roots of seed plants have three major functions: anchoring the plant to
the soil, absorbing water and minerals and transporting them upwards, and
storing the products of photosynthesis. Some roots are modified to absorb
moisture and exchange gases. Most roots are underground. Some plants,
however, also have adventitious roots, which emerge above the ground
from the shoot.
Types of Root Systems
Root systems are mainly of two types ([link]). Eudicots have a tap root
system, while monocots have a fibrous root system. A tap root system has
a main root that grows down vertically, and from which many smaller
lateral roots arise. Dandelions are a good example; their tap roots usually
break off when trying to pull these weeds, and they can regrow another
shoot from the remaining root). A tap root system penetrates deep into the
soil. In contrast, a fibrous root system is located closer to the soil surface,
and forms a dense network of roots that also helps prevent soil erosion
(lawn grasses are a good example, as are wheat, rice, and corn). Some
plants have a combination of tap roots and fibrous roots. Plants that grow in
dry areas often have deep root systems, whereas plants growing in areas
with abundant water are likely to have shallower root systems.
(a) Tap root systems have a main root that
grows down, while (b) fibrous root systems
consist of many small roots. (credit b:
modification of work by “Austen
Squarepants”/Flickr)
Root Growth and Anatomy
Root growth begins with seed germination. When the plant embryo emerges
from the seed, the radicle of the embryo forms the root system. The tip of
the root is protected by the root cap, a structure exclusive to roots and
unlike any other plant structure. The root cap is continuously replaced
because it gets damaged easily as the root pushes through soil. The root tip
can be divided into three zones: a zone of cell division, a zone of
elongation, and a zone of maturation and differentiation ({link]). The zone
of cell division is closest to the root tip; it is made up of the actively
dividing cells of the root meristem. The zone of elongation is where the
newly formed cells increase in length, thereby lengthening the root.
Beginning at the first root hair is the zone of cell maturation where the root
cells begin to differentiate into special cell types. All three zones are in the
first centimeter or so of the root tip.
Vascular
cylinder
Root hair
Area of
maturation
Area of
elongation
Apical
meristem
Area of
cell division
Root cap
A longitudinal view of the
root reveals the zones of cell
division, elongation, and
maturation. Cell division
occurs in the apical meristem.
The root has an outer layer of cells called the epidermis, which surrounds
areas of ground tissue and vascular tissue. The epidermis provides
protection and helps in absorption. Root hairs, which are extensions of root
epidermal cells, increase the surface area of the root, greatly contributing to
the absorption of water and minerals.
Inside the root, the ground tissue forms two regions: the cortex and the pith
({link]). Compared to stems, roots have lots of cortex and little pith. Both
regions include cells that store photosynthetic products. The cortex is
between the epidermis and the vascular tissue, whereas the pith lies
between the vascular tissue and the center of the root.
Exodermis
(sclerenchyma) Epidermis Phloem
Cortex Pericycle Endodermis Root hairs
(parenchyma cells)
Staining reveals different cell
types in this light micrograph of a
wheat (Triticum) root cross
section. Sclerenchyma cells of the
exodermis and xylem cells stain
red, and phloem cells stain blue.
Other cell types stain black. The
stele, or vascular tissue, is the area
inside endodermis (indicated by a
green ring). Root hairs are visible
outside the epidermis. (credit:
scale-bar data from Matt Russell)
The vascular tissue in the root is arranged in the inner portion of the root,
which is called the vascular cylinder ({link]). A layer of cells known as the
endodermis separates the vascular tissue from the ground tissue in the
outer portion of the root. The endodermis is exclusive to roots, and serves
as a checkpoint for materials entering the root’s vascular system. A waxy
substance called suberin is present on the walls of the endodermal cells.
This waxy region, known as the Casparian strip, forces water and solutes
to cross the plasma membranes of endodermal cells instead of slipping
between the cells. This ensures that only materials required by the root pass
through the endodermis, while toxic substances and pathogens are generally
excluded. The outermost cell layer of the root’s vascular tissue is the
pericycle, an area that can give rise to lateral roots. In eudicot roots, the
xylem and phloem are arranged alternately in an X shape, whereas in
monocot roots, the vascular tissue is arranged in a ring around the pith.
Eudicot root Monocot root
Epidermis ee es Pith
Pericycle
Endodermis
In (left) typical eudicots, the vascular tissue forms
an X shape in the center of the root. In (right)
typical monocots, the phloem cells and the larger
xylem cells form a characteristic ring around the
central pith.
Root Modifications
Root structures may be modified for specific purposes. For example, some
roots are bulbous and store starch. Aerial roots and prop roots are two forms
of aboveground roots that provide additional support to anchor the plant.
Tap roots, such as carrots, turnips, and beets, are examples of roots that are
modified for food storage ([link]).
Many vegetables are
modified roots.
Epiphytic roots enable a plant to grow on another plant. For example, the
epiphytic roots of orchids develop a spongy tissue to absorb moisture. The
banyan tree (Ficus sp.) begins as an epiphyte, germinating in the branches
of a host tree; aerial roots develop from the branches and eventually reach
the ground, providing additional support ([link]). In screwpine (Pandanus
sp.), a palm-like tree that grows in sandy tropical soils, aboveground prop
roots develop from the nodes to provide additional support.
The (a) banyan tree, also known as the strangler fig,
begins life as an epiphyte in a host tree. Aerial roots
extend to the ground and support the growing plant,
which eventually strangles the host tree. The (b)
screwpine develops aboveground roots that help
support the plant in sandy soils. (credit a: modification
of work by "psyberartist"/Flickr; credit b: modification
of work by David Eikhoff)
Leaves
Leaves are the main sites for photosynthesis: the process by which plants
synthesize food. Most leaves are usually green, due to the presence of
chlorophyll in the leaf cells. However, some leaves may have different
colors, caused by other plant pigments that mask the green chlorophyll.
The thickness, shape, and size of leaves are adapted to the environment.
Each variation helps a plant species maximize its chances of survival in a
particular habitat. Usually, the leaves of plants growing in tropical
rainforests have larger surface areas than those of plants growing in deserts
or very cold conditions, which are likely to have a smaller surface area to
minimize water loss.
Structure of a Typical Leaf
Each leaf typically has a leaf blade called the lamina, which is also the
widest part of the leaf. Some leaves are attached to the plant stem by a
petiole. Leaves that do not have a petiole and are directly attached to the
plant stem are called sessile leaves. Small green appendages usually found
at the base of the petiole are known as stipules. Most leaves have a midrib,
which travels the length of the leaf and branches to each side to produce
veins of vascular tissue. The edge of the leaf is called the margin. [link]
shows the structure of a typical eudicot leaf.
Deceptively simple in appearance,
a leaf is a highly efficient
structure.
Within each leaf, the vascular tissue forms veins. The arrangement of veins
in a leaf is called the venation pattern. Monocots and eudicots differ in their
patterns of venation ([link]). Monocots have parallel venation; the veins run
in straight lines across the length of the leaf without converging at a point.
In eudicots, however, the veins of the leaf have a net-like appearance,
forming a pattern known as reticulate venation. One extant plant, the
Ginkgo biloba, has dichotomous venation where the veins fork.
(a) (b) (c)
(a) Tulip (Tulipa), a monocot, has leaves with
parallel venation. The netlike venation in this (b)
linden (Tilia cordata) leaf distinguishes it as a
eudicot. The (c) Ginkgo biloba tree has dichotomous
venation. (credit a photo: modification of work by
“Drewboy64”/Wikimedia Commons; credit b photo:
modification of work by Roger Griffith; credit c
photo: modification of work by
"geishaboy500"/Flickr; credit abc illustrations:
modification of work by Agnieszka Kwiecien)
Leaf Structure and Function
The outermost layer of the leaf is the epidermis; it is present on both sides
of the leaf and is called the upper and lower epidermis, respectively. The
epidermis helps in the regulation of gas exchange. It contains stomata
({link]): openings through which the exchange of gases takes place. Two
guard cells surround each stoma, regulating its opening and closing.
Visualized at 500x with a scanning electron microscope, several
stomata are Clearly visible on (a) the surface of this sumac (Rhus
glabra) leaf. At 5,000x magnification, the guard cells of (b) a
single stoma from lyre-leaved sand cress (Arabidopsis lyrata)
have the appearance of lips that surround the opening. In this (c)
light micrograph cross-section of an A. lyrata leaf, the guard cell
pair is visible along with the large, sub-stomatal air space in the
leaf. (credit: modification of work by Robert R. Wise; part c scale-
bar data from Matt Russell)
When a plant has sufficient amount of water and sunlight, guard cells
accumulate potassium (K*) ions, and water flows into the guard cells by
osmosis. The movement of water into the guard cells causes the cells to
swell and become turgid. As the cells become more turgid, the inner thick
cell wall does not stretch as much as the thin outer cell wall, and this causes
a space to form between the two guard cells opening the stoma. When the
plant closes that stoma, K* ions leave the guard cells, and water follows by
osmosis. The movement of water out of the guard cells causes the cells to
shrink and become flaccid thereby closing the stoma. [link] is an illustration
of how guard cells open and close the stoma.
Closed Stomata
Flaccid guard cells
cell wall cell wall
Open Stomata
Turgid guard cells
Thick Thin
cell wall cell wall
The movement of potassium ions (K*) into and
out of the guard cells allows the plant to either
open or close its stomata. Work by Robert A.
Bear
The movement of K” ions into or out of the guard cell as currently
hypothesized is a passive process and related to the active transport of H*
ions in the opposite direction of the movement of the K* ions. So, when H*
ions are actively pumped out of the guard cell, K* ions move into the guard
cell passively flowing down an electrical gradient created by the H” ions.
Since the plant uses energy to open and close the stomata, the benefits of
regulating the opening and closing of the stomata are greater than the
energy expenditure of moving ions into and out of the guard cells. Plants
actively regulate the movement of these ions and can respond rapidly to
changes in the amount of sunlight, relative humidity and carbon dioxide.
The epidermis is usually one cell layer thick; however, in plants that grow
in very hot or very cold conditions, the epidermis may be several layers
thick to protect against excessive water loss from transpiration. A waxy
layer known as the cuticle covers the leaves of all plant species. The cuticle
reduces the rate of water loss from the leaf surface. Other leaves may have
small hairs (trichomes) on the leaf surface. Trichomes help to deter
herbivory by restricting insect movements, or by storing toxic or bad-tasting
compounds; they can also reduce the rate of transpiration by blocking air
flow across the leaf surface ([link]).
a
Ie
~é
_ 125 pm
gt
Trichomes give leaves a fuzzy appearance as in this (a) sundew
(Drosera sp.). Leaf trichomes include (b) branched trichomes
on the leaf of Arabidopsis lyrata and (c) multibranched
trichomes on a mature Quercus marilandica leaf. (credit a:
John Freeland; credit b, c: modification of work by Robert R.
Wise; scale-bar data from Matt Russell)
Below the epidermis of eudicot leaves are layers of cells known as the
mesophyll, or “middle leaf.” The mesophyll of most leaves typically
contains two arrangements of parenchyma cells: the palisade parenchyma
and spongy parenchyma ([link]). The palisade parenchyma (also called the
palisade mesophyll) has column-shaped, tightly packed cells, and may be
present in one, two, or three layers. Below the palisade parenchyma are
loosely arranged cells of an irregular shape. These are the cells of the
spongy parenchyma (or spongy mesophyll). The air space found between
the spongy parenchyma cells allows gaseous exchange between the leaf and
the outside atmosphere through the stomata. In aquatic plants, the
intercellular spaces in the spongy parenchyma help the leaf float. Both
layers of the mesophyll contain many chloroplasts. Guard cells are the only
epidermal cells to contain chloroplasts.
Cuticle
Upper
epidermis
Palisade parenchyma
Mesophyll
Spongy parenchyma
Lower
epidermis
Cuticle
Guard cells
200 um
In the (a) leaf drawing, the central
mesophyll is sandwiched between an
upper and lower epidermis. The
mesophyll has two layers: an upper
palisade layer comprised of tightly
packed, columnar cells, and a lower
spongy layer, comprised of loosely
packed, irregularly shaped cells. Stomata
on the leaf underside allow gas
exchange. A waxy cuticle covers all
aerial surfaces of land plants to minimize
water loss. These leaf layers are clearly
visible in the (b) scanning electron
micrograph. The numerous small bumps
in the palisade parenchyma cells are
chloroplasts. Chloroplasts are also
present in the spongy parenchyma, but
are not as obvious. The bumps
protruding from the lower surface of the
leave are glandular trichomes, which
differ in structure from the stalked
trichomes in [link]. (credit b:
modification of work by Robert R. Wise)
Like the stem, the leaf contains vascular bundles composed of xylem and
phloem ({link]). The xylem consists of tracheids and vessels, which
transport water and minerals to the leaves. The phloem transports the
photosynthetic products from the leaf to the other parts of the plant. A
single vascular bundle, no matter how large or small, always contains both
xylem and phloem tissues.
This scanning electron micrograph
shows xylem and phloem in the leaf
vascular bundle from the lyre-leaved
sand cress (Arabidopsis lyrata).
(credit: modification of work by
Robert R. Wise; scale-bar data from
Matt Russell)
Leaf Adaptations
Coniferous plant species that thrive in cold environments, like spruce, fir,
and pine, have leaves that are reduced in size and needle-like in appearance.
These needle-like leaves have sunken stomata and a smaller surface area:
two attributes that aid in reducing water loss. In hot climates, plants such as
cacti have succulent leaves that help to conserve water. Many aquatic plants
have leaves with wide lamina that can float on the surface of the water, and
a thick waxy cuticle on the leaf surface that repels water.
Note:
Evolution Connection
Plant Adaptations in Resource-Deficient Environments
Roots, stems, and leaves are structured to ensure that a plant can obtain the
required resources of sunlight, water, soil nutrients, carbon dioxide and
oxygen. Some remarkable adaptations have evolved to enable plant species
to thrive in less than ideal habitats, where one or more of these resources is
in short supply.
In tropical rainforests, light is often scarce, since many trees and plants
grow Close together and block much of the sunlight from reaching the
forest floor. Many tropical plant species have exceptionally broad leaves to
maximize the capture of sunlight. Other species are epiphytes: plants that
grow on other plants that serve as a physical support. Such plants are able
to grow high up in the canopy atop the branches of other trees, where
sunlight is more plentiful. Epiphytes live on rain and minerals collected in
the branches and leaves of the supporting plant. Bromeliads (members of
the pineapple family), ferns, and orchids are examples of tropical epiphytes
({link]). Many epiphytes have specialized tissues that enable them to
efficiently capture and store water.
x
One of the most well
known bromeliads is
Spanish moss (Tillandsia
usneoides), seen here in
an Oak tree. (credit:
Kristine Paulus)
Some plants have special adaptations that help them to survive in nutrient-
poor environments. Carnivorous plants, such as the Venus flytrap and the
pitcher plant ([link]), grow in bogs where the soil is low in nitrogen. In
these plants, leaves are modified to capture insects. The insect-capturing
leaves may have evolved to provide these plants with a supplementary
source of much-needed nitrogen.
(a) (b)
The (a) Venus flytrap has modified leaves that can
capture insects. When an unlucky insect touches
the trigger hairs inside the leaf, the trap suddenly
closes. The opening of the (b) pitcher plant is lined
with a slippery wax. Insects crawling on the lip
slip and fall into a pool of water in the bottom of
the pitcher, where they are digested by bacteria.
The plant then absorbs the smaller molecules.
(credit a: modification of work by Peter Shanks;
credit b: modification of work by Tim Mansfield)
Many swamp plants have adaptations that enable them to thrive in wet
areas, where their roots grow submerged underwater. In these aquatic
areas, the soil is unstable and little oxygen is available to reach the roots.
Trees such as mangroves (Rhizophora sp.) growing in coastal waters
produce aboveground roots that help support the tree ([link]). Some species
of mangroves, as well as cypress trees, have pneumatophores: upward-
growing roots containing pores and pockets of tissue specialized for gas
exchange. Wild rice is an aquatic plant with large air spaces in the root
cortex. The air-filled tissue—called aerenchyma—provides a path for
oxygen to diffuse down to the root tips, which are embedded in oxygen-
poor bottom sediments.
(a) (b) (c)
The branches of (a) mangrove trees develop aerial roots, which
descend to the ground and help to anchor the trees. (b) Cypress
trees and some mangrove species have upward-growing roots
called pneumatophores that are involved in gas exchange.
Aquatic plants such as (c) wild rice have large spaces in the
root cortex called aerenchyma, visualized here using scanning
electron microscopy. (credit a: modification of work by
Roberto Verzo; credit b: modification of work by Duane
Burdick; credit c: modification of work by Robert R. Wise)
Transport of Water and Solutes in Plants
""What else is the function of a forest, first and foremost, if not a place to
do this: to capture and filter water and merge with sunlight, to create
intricate being, intricate matter?"" Rick Bass, "The Larch", Orion
Magazine, September/October 2012
"The ability of trees to suck water from roots to leaves, sometimes to
heights of over a hundred meters, is remarkable given the absence of any
mechanical pump" wrote Harvey R. Brown in a review article in Physics in
Perspective in 2013. Scientists have discovered quite a lot about this
remarkable process, but that makes it no less remarkable. The structure of
plant roots, stems, and leaves facilitates the transport of water, nutrients,
and photosynthates throughout the plant. The phloem and xylem are the
main tissues responsible for this movement. Water potential,
evapotranspiration, and stomatal regulation influence how water and
nutrients are transported in plants. To understand how these processes work,
we must first understand the energetics of water potential.
Water Potential
Plants are phenomenal hydraulic engineers. Using only the basic laws of
physics and the simple manipulation of potential energy, plants can move
water to the top of a 116-meter-tall tree ([link]a). Plants can also use
hydraulics to generate enough force to split rocks and buckle sidewalks
({link |b). Plants achieve this because of water potential.
(b)
With heights nearing 116 meters, (a) coast
redwoods (Sequoia sempervirens) are the tallest
trees in the world. Plant roots can easily generate
enough force to (b) buckle and break concrete
sidewalks, much to the dismay of homeowners and
city maintenance departments. (credit a:
modification of work by Bernt Rostad; credit b:
modification of work by Pedestrians Educating
Drivers on Safety, Inc.)
Water potential is a measure of the potential energy in water. Plant
physiologists are not interested in the energy in any one particular aqueous
system, but are very interested in water movement between two systems. In
practical terms, therefore, water potential is the difference in potential
energy between a given water sample and pure water (at atmospheric
pressure and ambient temperature). Water potential is expressed in units of
pressure (pressure is a form of energy) called megapascals (MPa). The
potential of pure water is, by convenience of definition, designated a value
of zero (even though pure water contains plenty of potential energy, that
energy is ignored). Water potential values for the water in a plant root, stem,
or leaf are therefore expressed relative to pure HO.
The water potential in plant solutions is influenced by solute concentration,
pressure, gravity, and factors called matrix effects. “System” can refer to the
water potential of the soil water, root water, stem water, leaf water or the
water in the atmosphere: whichever aqueous system is under consideration.
As the individual components change, they raise or lower the total water
potential of a system. When this happens, water moves to equilibrate,
moving from the system or compartment with a higher water potential to
the system or compartment with a lower water potential. This brings the
difference in water potential between the two systems back to zero.
Therefore, for water to move through the plant from the soil to the air (a
process called transpiration), the water potential of the soil water > root
water > stem water > leaf water > atmosphere water.
Water only moves in response to changes in water potential, not in response
to the individual components. However, because the individual components
influence the total water potential of the system, by manipulating the
individual components solute concentration, a plant can control water
movement.
Solute Potential
Solute potential, also called osmotic potential, is negative in a plant cell and
zero in distilled water. Typical values for cell cytoplasm are —0.5 to —1.0
MPa. Solutes reduce water potential (resulting in a negative water potential)
by consuming some of the potential energy available in the water. The
internal water potential of a plant cell is more negative than pure water
because of the cytoplasm’s high solute content ({link]). Because of this
difference in water potential water will move from the soil into a plant’s
root cells via the process of osmosis. This is why solute potential is
sometimes called osmotic potential.
H,0
Pure water
Positive Negative
pressure pressure
H,0 H,0 H,0
<< <—_
Solute
~__ ~~
Adding solute to the Applying positive Applying negative
right side lowers ., pressure to the left pressure to the left
Causing water to side increases Wp, side lowers Wp,
move to the right causing water to causing water to
side of the tube. move to the right move to the left side
side of the tube. of the tube.
In this example with a semipermeable
membrane between two aqueous systems,
water will move from a region of higher to
lower water potential until equilibrium is
reached. Solutes (W,), pressure (P,), and
gravity (‘Y,) influence total water potential
for each side of the tube (Wotqy M82 He"),
and therefore, the difference between Viotai
on each side (AV). (,, , the potential due to
interaction of water with solid substrates, is
ignored in this example because glass is not
especially hydrophilic). Water moves in
response to the difference in water potential
between two systems (the left and right sides
of the tube).
Pressure Potential
Pressure potential, also called turgor potential, may be positive or negative
({link]). Because pressure is an expression of energy, the higher the
pressure, the more potential energy in a system, and vice versa. An example
of the effect of turgor pressure is the wilting of leaves and their restoration
after the plant has been watered ((link]). Water lost from the leaves via
transpiration is restored by uptake via the roots.
A plant can manipulate turgor pressure via its ability to manipulate solute
concentration and by the process of osmosis. If a plant cell increases the
cytoplasmic solute concentration water will move into the cell by osmosis.
Turgor pressure is also under indirect plant control via the opening and
closing of stomata. Stomatal openings allow water to evaporate from the
leaf, reducing the water potential of the leaf and increasing it between the
water in the leaf and the petiole, thereby allowing water to flow from the
petiole into the leaf.
(a) (b)
When (a) total water potential (Wotai) is
lower outside the cells than inside, water
moves out of the cells and the plant wilts.
When (b) the total water potential is higher
outside the plant cells than inside, water
moves into the cells, resulting in turgor
pressure (‘¥,) and keeping the plant erect.
(credit: modification of work by Victor M.
Vicente Selvas)
Gravity Potential
Gravity potential is always negative to zero in a plant with no height. It
always removes or consumes potential energy from the system. The force of
gravity pulls water downwards to the soil, reducing the total amount of
potential energy in the water in the plan. The taller the plant, the taller the
water column, and the more influence gravity has. On a cellular scale and in
short plants, this effect is negligible and easily ignored. However, over the
height of a tall tree like a coast redwood, the gravitational pull of -O.1 MPa
is equivalent to an extra 1 MPa of resistance that must be overcome for
water to reach the leaves of the tallest trees.
Matric Potential
The binding of water to a matrix of surrounding substances always removes
or consumes potential energy from the system. Matric potential is similar to
solute potential because it involves tying up the energy in an aqueous
system by forming hydrogen bonds between the water and some other
component. Matric potential is always negative to zero. In a dry system, it
can be as low as —2 MPa in a dry seed, and it is zero in a water-saturated
system.
Movement of Water and Minerals in the Xylem
Solutes, pressure, gravity, and matric potential are all important for the
transport of water in plants. Water moves from an area of higher total water
potential (higher Gibbs free energy) to an area of lower total water
potential. Gibbs free energy is the energy associated with a chemical
reaction that can be used to do work.
Transpiration is the loss of water from the plant through evaporation at the
leaf surface. It is the main driver of water movement in the xylem.
Transpiration is caused by the evaporation of water at the leaf—atmosphere
interface; it creates negative pressure (tension) equivalent to —2 MPa at the
leaf surface. This value varies greatly depending on the vapor pressure
deficit, which can be negligible at high relative humidity and substantial at
low relative humidity. Water from the roots is pulled up by this tension. At
night, when stomata shut and transpiration stops, the water is held in the
stem and leaf by the adhesion of water to the cell walls of the xylem vessels
and tracheids, and the cohesion of water molecules to each other. This is
called the cohesion—tension theory of sap ascent.
Inside the leaf at the cellular level, water on the surface of mesophyll cells
saturates the cellulose microfibrils of the primary cell wall. The leaf
contains many large intercellular air spaces for the exchange of oxygen for
carbon dioxide, which is required for photosynthesis. The wet cell wall is
exposed to this leaf internal air space, and the water on the surface of the
cells evaporates into the air spaces, decreasing the thin film on the surface
of the mesophyll cells. This decrease creates a greater tension on the water
in the mesophyll cells ({link]), thereby increasing the pull on the water in
the xylem vessels. The xylem vessels and tracheids are structurally adapted
to cope with large changes in pressure. Rings in the vessels maintain their
tubular shape, much like the rings on a vacuum cleaner hose keep the hose
open while it is under pressure. Small perforations between vessel elements
reduce the number and size of gas bubbles that can form via a process
called cavitation. The formation of gas bubbles in xylem interrupts the
continuous stream of water from the base to the top of the plant, causing a
break termed an embolism in the flow of xylem sap. The taller the tree, the
greater the tension forces needed to pull water, and the more cavitation
events. In larger trees, the resulting embolisms can plug xylem vessels,
making them non-functional.
60000 00
Atmosphere:
~-100 MPa
Transpiration draws Low
water from the leaf.
Leaf at tip of tree:
~-1.5 MPa
Water potential gradient
Cohesion and adhesion
draw water up the xylem.
Stem:~-0.6 MPa
Root hairs
Root cells: ~—0.2 MPa
Soil particle
Water molecule
Xylem
draws water into the root.
The cohesion—tension theory of sap
ascent is shown. Evaporation from the
mesophyll cells produces a negative
water potential gradient that causes
water to move upwards from the roots
through the xylem.
Transpiration is a passive process, meaning that metabolic energy in the
form of ATP is not required for water movement. The energy driving
transpiration is the difference in energy between the water in the soil and
the water in the atmosphere. However, transpiration is tightly controlled.
Control of Transpiration
The atmosphere to which the leaf is exposed drives transpiration, but also
causes massive water loss from the plant. Up to 90 percent of the water
taken up by roots may be lost through transpiration.
Leaves are covered by a waxy cuticle on the outer surface that prevents the
loss of water. Regulation of transpiration, therefore, is achieved primarily
through the opening and closing of stomata on the leaf surface. Stomata are
surrounded by two specialized cells called guard cells, which open and
close in response to environmental cues such as light intensity and quality,
leaf water status, and carbon dioxide concentrations. Stomata must open to
allow air containing carbon dioxide and oxygen to diffuse into the leaf for
photosynthesis and respiration. When stomata are open, however, water
vapor is lost to the external environment, increasing the rate of
transpiration. Therefore, plants must maintain a balance between efficient
photosynthesis and water loss.
Plants have evolved over time to adapt to their local environment and
reduce transpiration (({link]). Desert plant (xerophytes) and plants that grow
on other plants (epiphytes) have limited access to water. Such plants usually
have a much thicker waxy cuticle than those growing in more moderate,
well-watered environments (mesophytes). Aquatic plants (hydrophytes)
also have their own set of anatomical and morphological leaf adaptations.
(c) (d)
Plants are suited to their local environment.
(a) Xerophytes, like this prickly pear cactus
(Opuntia sp.) and (b) epiphytes such as this
tropical Aeschynanthus perrottetii have
adapted to very limited water resources. The
leaves of a prickly pear are modified into
spines, which lowers the surface-to-volume
ratio and reduces water loss. Photosynthesis
takes place in the stem, which also stores
water. (b) A. perottetii leaves have a waxy
cuticle that prevents water loss. (c)
Goldenrod (Solidago sp.) is a mesophyte,
well suited for moderate environments. (d)
Hydrophytes, like this fragrant water lily
(Nymphaea odorata), are adapted to thrive
in aquatic environments. (credit a:
modification of work by Jon Sullivan; credit
b: modification of work by L.
Shyamal/Wikimedia Commons; credit c:
modification of work by Huw Williams;
credit d: modification of work by Jason
Hollinger)
Xerophytes and epiphytes often have a thick covering of trichomes or of
stomata that are sunken below the leaf’s surface. Trichomes are specialized
hair-like epidermal cells that secrete oils and substances. These adaptations
impede air flow across the stomatal pore and reduce transpiration. Multiple
epidermal layers are also commonly found in these types of plants.
Transportation of Photosynthates in the Phloem
Plants need an energy source to grow. In seeds and bulbs, food is stored in
polymers (such as starch) that are converted by metabolic processes into
sucrose for newly developing plants. Once green shoots and leaves are
growing, plants are able to produce their own food by photosynthesizing.
The products of photosynthesis are called photosynthates, which are usually
in the form of simple sugars such as sucrose.
Structures that produce photosynthates for the growing plant are referred to
as sources. Sugars produced in sources, such as leaves, need to be delivered
to growing parts of the plant via the phloem in a process called
translocation. The points of sugar delivery, such as roots, young shoots, and
developing seeds, are called sinks. Seeds, tubers, and bulbs can be either a
source or a sink, depending on the plant’s stage of development and the
season.
The products from the source are usually moved (translocated) to the
nearest sink through the phloem. For example, the highest leaves will send
photosynthates upward to the growing shoot tip, whereas lower leaves will
direct photosynthates downward to the roots. Intermediate leaves will send
products in both directions, unlike the flow in the xylem, which is always
unidirectional (soil to leaf to atmosphere). The pattern of photosynthate
flow changes as the plant grows and develops. Photosynthates are directed
primarily to the roots early on, to shoots and leaves during vegetative
growth, and to seeds and fruits during reproductive development. They are
also directed to tubers for storage.
Pressure Flow Model: Transport from Source to Sink
Photosynthates, such as sucrose, are produced in the mesophyll cells of
photosynthesizing leaves. From there they are translocated through the
phloem to where they are used or stored. Mesophyll cells are connected by
cytoplasmic channels called plasmodesmata. Photosynthates move through
these channels to reach phloem sieve-tube elements (STEs) in the vascular
bundles. From the mesophyll cells, the photosynthates are loaded into the
phloem STEs. The sucrose is actively transported against its concentration
gradient (a process requiring ATP) into the phloem cells using the
electrochemical potential of the proton gradient. This is coupled to the
uptake of sucrose with a carrier protein called the sucrose-H* symporter.
Phloem STEs have reduced cytoplasmic contents, and are connected by a
sieve plate with pores that allow for pressure-driven bulk flow, or
translocation, of phloem sap. Companion cells are associated with STEs.
They assist with metabolic activities and produce energy for the STEs
({link]).
Sieve tube
element
Companion
cell
Lateral sieve
area
Sieve tube
plate
Phloem is comprised
of cells called sieve-
tube elements. Phloem
sap travels through
perforations called
sieve tube plates.
Neighboring
companion cells carry
out metabolic
functions for the sieve-
tube elements and
provide them with
energy. Lateral sieve
areas connect the
sieve-tube elements to
the companion cells.
Once in the phloem, the photosynthates are translocated to the closest sink.
Phloem sap is an aqueous solution that contains up to 30 percent sugar,
minerals, amino acids, and plant growth regulators. The high percentage of
sugar Causes water to move by osmosis from the adjacent xylem into the
phloem tubes, thereby increasing pressure. This increase in total water
potential causes the bulk flow of phloem from source to sink ([link]).
Sucrose concentration in the sink cells is lower than in the phloem STEs
because the sink sucrose has been metabolized for growth, or converted to
starch for storage or other polymers, such as cellulose, for structural
integrity. Unloading at the sink end of the phloem tube occurs by either
diffusion or active transport of sucrose molecules from an area of high
concentration to one of low concentration. Water diffuses from the phloem
by osmosis and is then transpired or recycled via the xylem back into the
phloem sap. This concept of how photosynthates move from the source to
the sink is called the pressure flow model.
Companion
cell
Source cell
(leaf)
Sink cell
(root)
Sucrose is actively
transported from source
cells into companion
cells and then into the
sieve-tube elements.
This reduces the water
potential, which causes
water to enter the
phloem from the xylem.
The resulting positive
pressure forces the
sucrose-water mixture
down toward the roots,
where sucrose is
unloaded. Transpiration
causes water to return to
the leaves through the
xylem vessels.
Nutritional Requirements of Plants
"T died as mineral and became a plant," "I died as plant and rose to animal,"
"I died as animal and became man." "Why should I fear? When was I less
by dying?" Jalal ad-Din ar-Rumi, Sufi poet (1207-73)
Rumi's musings on minerals and plants contain a kernel of truth. Minerals
become incorporated into the plant body, and are critically important in
plant function. Plants are unique organisms that can absorb nutrients and
water through their root system, as well as carbon dioxide from the
atmosphere. Soil quality and climate are the major determinants of plant
distribution and growth. The combination of soil nutrients, water, and
carbon dioxide, along with sunlight, allows plants to grow.
The Chemical Composition of Plants
Since plants require nutrients in the form of elements such as carbon and
potassium, it is important to understand the chemical composition of plants.
The majority of volume in a plant cell is water; it typically comprises 80 to
90 percent of the plant’s total weight. Soil is the water source for land
plants, and can be an abundant source of water, even if it appears dry. Plant
roots absorb water from the soil through root hairs and transport it up to the
leaves through the xylem. As water vapor is lost from the leaves, the
process of transpiration and the polarity of water molecules (which enables
them to form hydrogen bonds) draws more water from the roots up through
the plant to the leaves ([link]). Plants need water to support cell structure,
for metabolic functions, to carry nutrients, and for photosynthesis.
Root hairs
Water is absorbed through the
root hairs and moves up the
xylem to the leaves.
Plant cells need essential substances, collectively called nutrients, to sustain
life. Plant nutrients may be composed of either organic or inorganic
compounds. An organic compound is a chemical compound that contains
carbon, such as carbon dioxide obtained from the atmosphere. Carbon that
was obtained from atmospheric CO, composes the majority of the dry mass
within most plants. An inorganic compound does not contain carbon and
is not part of, or produced by, a living organism. Inorganic substances,
which form the majority of the soil solution, are commonly called minerals:
those required by plants include nitrogen (N) and potassium (K) for
structure and regulation.
Essential Nutrients
Plants require only light, water and about 20 elements to support all their
biochemical needs: these 20 elements are called essential nutrients ([link]).
For an element to be regarded as essential, three criteria are required: 1) a
plant cannot complete its life cycle without the element; 2) no other element
can perform the function of the element; and 3) the element is directly
involved in plant nutrition.
Essential Elements for Plant Growth
Macronutrients
Carbon (C)
Hydrogen (H)
Oxygen (O)
Nitrogen (N)
Phosphorus (P)
Potassium (K)
Calcium (Ca)
Magnesium (Mg)
Sulfur (S)
Micronutrients
Iron (Fe)
Manganese (Mn)
Boron (B)
Molybdenum (Mo)
Copper (Cu)
Zinc (Zn)
Chlorine (Cl)
Nickel (Ni)
Cobalt (Co)
Sodium (S)
Silicon (Si)
Macronutrients and Micronutrients
The essential elements can be divided into two groups: macronutrients and
micronutrients. Nutrients that plants require in larger amounts are called
macronutrients. About half of the essential elements are considered
macronutrients: carbon, hydrogen, oxygen, nitrogen, phosphorus,
potassium, calcium, magnesium and sulfur. The first of these
macronutrients, carbon (C), is required to form carbohydrates, proteins,
nucleic acids, and many other compounds; it is therefore present in all
macromolecules. On average, the dry weight (excluding water) of a cell is
50 percent carbon. As shown in [link], carbon is a key part of plant
biomolecules.
Cellulose fibers
Cellulose structure
Cellulose, the main structural component of the
plant cell wall, makes up over thirty percent of
plant matter. It is the most abundant organic
compound on earth. Plants are able to make
their own cellulose, but need carbon from the
soil to do so.
The next most abundant element in plant cells is nitrogen (N); it is part of
proteins and nucleic acids. Nitrogen is also used in the synthesis of some
vitamins. Hydrogen and oxygen are macronutrients that are part of many
organic compounds, and also form water. Oxygen is necessary for cellular
respiration; plants use oxygen to store energy in the form of ATP.
Phosphorus (P), another macromolecule, is necessary to synthesize nucleic
acids and phospholipids. As part of ATP, phosphorus enables food energy to
be converted into chemical energy through oxidative phosphorylation.
Likewise, light energy is converted into chemical energy during
photophosphorylation in photosynthesis, and into chemical energy to be
extracted during respiration. Sulfur is part of certain amino acids, such as
cysteine and methionine, and is present in several coenzymes. Sulfur also
plays a role in photosynthesis as part of the electron transport chain, where
hydrogen gradients play a key role in the conversion of light energy into
ATP. Potassium (K) is important because of its role in regulating stomatal
opening and closing. As the openings for gas exchange, stomata help
maintain a healthy water balance; a potassium ion pump supports this
process.
Magnesium (Mg) and calcium (Ca) are also important macronutrients. The
role of calcium is twofold: to regulate nutrient transport, and to support
many enzyme functions. Magnesium is important to the photosynthetic
process. These minerals, along with the micronutrients, which are described
below, also contribute to the plant’s ionic balance.
In addition to macronutrients, organisms require various elements in small
amounts. These micronutrients, or trace elements, are present in very
small quantities. They include boron (B), chlorine (Cl), manganese (Mn),
iron (Fe), zinc (Zn), copper (Cu), molybdenum (Mo), nickel (Ni), silicon
(Si), and sodium (Na).
Deficiencies in any of these nutrients—particularly the macronutrients—
can adversely affect plant growth ([Llink]. Depending on the specific
nutrient, a lack can cause stunted growth, slow growth, or chlorosis
(yellowing of the leaves). Extreme deficiencies may result in leaves
showing signs of cell death.
Nutrient deficiency is evident in the symptoms
these plants show. This (a) grape tomato suffers
from blossom end rot caused by calcium
deficiency. The yellowing in this (b) Frangula
alnus results from magnesium deficiency.
Inadequate magnesium also leads to (c)
intervenal chlorosis, seen here in a sweetgum
leaf. This (d) palm is affected by potassium
deficiency. (credit c: modification of work by
Jim Conrad; credit d: modification of work by
Malcolm Manners)
Nutritional Adaptations of Plants
B
Introduction
"The fixation of atmospheric nitrogen is one of the great discoveries,
awaiting the genius of chemists." Sir William Crookes Presidential Address
to the British Association for the Advancement of Science, 1898
Of course, plants discovered how to fix nitrogen (convert N> gas to a form
that can be incorporated in biological molecules such as nucleic acids and
proteins) a long time ago. Or rather, they recruited nitrogen-fixing bacteria
into a mutualistic relationship, where the bacteria fix nitrogen and provide
nitrogen-containing compounds to the plant in exchange for food and
shelter.
Plants may also enlist the help of other microbial partners in nutrient
acquisition. Particular species of bacteria and fungi have evolved along with
certain plants to create a mutualistic symbiotic relationship with roots. This
improves the nutrition of both the plant and the microbe. The formation of
bacteria-containing nodules on the roots for nitrogen fixation, or the
association of mycorrhizal fungi with roots for enhanced nutrient and water
uptake, can be considered among the nutritional adaptations of plants.
However, these are not the only type of adaptations that we may find; many
plants have other adaptations that allow them to thrive under specific
conditions.
Nitrogen Fixation: Root and Bacteria Interactions
Nitrogen is an important macronutrient because it is part of nucleic acids
and proteins. Atmospheric nitrogen, which is the diatomic molecule N» or
dinitrogen, is the largest pool of nitrogen in terrestrial ecosystems.
However, plants cannot take advantage of this nitrogen because they do not
have the necessary enzymes to convert it into biologically useful forms.
However, nitrogen can be “fixed,” which means that it can be converted to
ammonia (NH3) through biological, physical, or chemical processes. As you
have learned, biological nitrogen fixation is the conversion of atmospheric
nitrogen (N>) into ammonia (NHs3), exclusively carried out by prokaryotes
such as soil bacteria or cyanobacteria. Biological processes contribute 65
percent of the nitrogen used in agriculture.
(a) (b) (c)
Some common edible legumes—like (a) peanuts, (b)
beans, and (c) chickpeas—are able to interact
symbiotically with soil bacteria that fix nitrogen. (credit
a: modification of work by Jules Clancy; credit b:
modification of work by USDA)
Nitrogen-fixing soil bacteria, collectively called rhizobia, symbiotically
interact with legume roots to form specialized structures called nodules, in
which nitrogen fixation takes place. This process entails the reduction of
atmospheric nitrogen to ammonia, by means of the enzyme nitrogenase.
Therefore, using rhizobia is a natural and environmentally friendly way to
fertilize plants, as opposed to chemical fertilization that uses a
nonrenewable resource, such as natural gas. Through symbiotic nitrogen
fixation, the plant benefits from using an endless source of nitrogen from
the atmosphere. The process simultaneously contributes to soil fertility
because the plant root system leaves behind some of the biologically
available nitrogen. As in any symbiosis, both organisms benefit from the
interaction: the plant obtains ammonia, and bacteria obtain carbon
compounds generated through photosynthesis, as well as a protected niche
in which to grow ((Link]).
Rhizobia inside vesicles
Nitrogen-fixing nodules
Soybean roots contain (a) nitrogen-fixing nodules.
Cells within the nodules are infected with
Bradyrhyzobium japonicum, a rhizobia or “root-
loving” bacterium. The bacteria are encased in (b)
vesicles inside the cell, as can be seen in this
transmission electron micrograph. (credit a:
modification of work by USDA; credit b:
modification of work by Louisa Howard, Dartmouth
Electron Microscope Facility; scale-bar data from
Matt Russell)
Mycorrhizae: The Symbiotic Relationship between Fungi and
Roots
A nutrient depletion zone can develop when there is rapid soil solution
uptake, low nutrient concentration, low diffusion rate, or low soil moisture.
These conditions are very common; therefore, most plants rely on fungi to
facilitate the uptake of minerals from the soil. Fungi form symbiotic
associations called mycorrhizae with plant roots, in which the fungi actually
are integrated into the physical structure of the root. The fungi colonize the
living root tissue during active plant growth.
Through mycorrhization, the plant obtains mainly phosphate and other
minerals, such as zinc and copper, from the soil. The fungus obtains
nutrients, such as sugars, from the plant root ({link]). Mycorrhizae help
increase the surface area of the plant root system because hyphae, which are
narrow, can spread beyond the nutrient depletion zone. Hyphae can grow
into small soil pores that allow access to phosphorus that would otherwise
be unavailable to the plant. The beneficial effect on the plant is best
observed in poor soils. The benefit to fungi is that they can obtain up to 20
percent of the total carbon accessed by plants. Mycorrhizae functions as a
physical barrier to pathogens. It also provides an induction of generalized
host defense mechanisms, and sometimes involves production of antibiotic
compounds by the fungi.
Root tips proliferate in the
presence of mycorrhizal infection,
which appears as off-white fuzz in
this image. (credit: modification of
work by Nilsson et al., BMC
Bioinformatics 2005)
There are two types of mycorrhizae: ectomycorrhizae and
endomycorrhizae. Ectomycorrhizae form an extensive dense sheath around
the roots, called a mantle. Hyphae from the fungi extend from the mantle
into the soil, which increases the surface area for water and mineral
absorption. This type of mycorrhizae is found in forest trees, especially
conifers, birches, and oaks. Endomycorrhizae, also called arbuscular
mycorrhizae, do not form a dense sheath over the root. Instead, the fungal
mycelium is embedded within the root tissue. Endomycorrhizae are found
in the roots of more than 80 percent of terrestrial plants.
Nutrients from Other Sources
Some plants cannot produce their own food and must obtain their nutrition
from outside sources. This may occur with plants that are parasitic or
saprophytic. Some plants are mutualistic symbionts, epiphytes, or
insectivorous.
Plant Parasites
A parasitic plant depends on its host for survival. Some parasitic plants
have no leaves. An example of this is the dodder ({link]), which has a weak,
cylindrical stem that coils around the host and forms suckers. From these
suckers, cells invade the host stem and grow to connect with the vascular
bundles of the host. The parasitic plant obtains water and nutrients through
these connections. The plant is a total parasite (a holoparasite) because it is
completely dependent on its host. Other parasitic plants (hemiparasites) are
fully photosynthetic and only use the host for water and minerals. There are
about 4,100 species of parasitic plants.
The dodder is a holoparasite that
penetrates the host’s vascular
tissue and diverts nutrients for its
own growth. Note that the vines of
the dodder, which has white
flowers, are beige. The dodder has
no chlorophyll and cannot produce
its own food. (credit:
"Lalithamba"/Flickr)
Saprophytes
A saprophyte is a plant that does not have chlorophyll and gets its food
from dead matter, similar to bacteria and fungi (note that fungi are often
called saprophytes, which is incorrect, because fungi are not plants). Plants
like these use enzymes to convert organic food materials into simpler forms
from which they can absorb nutrients ({link]). Most saprophytes do not
directly digest dead matter: instead, they parasitize fungi that digest dead
matter, or are mycorrhizal, ultimately obtaining photosynthate from a
fungus that derived photosynthate from its host. Saprophytic plants are
uncommon; only a few species are described.
Saprophytes, like this Spotted Coralroot
(Corallorhiza maculata), obtain their food
from the mycelium of soil fungi, and do not
have chlorophyll. The Spotted Coralroot is
found in montane forests in northern and
western North America and Central
America. This specimen was photographed
in the Pecos Wilderness area in New
Mexico. (credit: photo by D. A. Rintoul)
Epiphytes
An epiphyte is a plant that grows on other plants, but is not dependent upon
the other plant for nutrition ({link]). Epiphytes have two types of roots:
clinging aerial roots, which absorb nutrients from humus that accumulates
in the crevices of trees; and aerial roots, which absorb moisture from the
atmosphere.
These epiphyte plants
grow in the main
greenhouse of the Jardin
des Plantes in Paris.
Insectivorous Plants
An insectivorous plant has specialized leaves to attract and digest insects.
You are probably familiar with the Venus flytrap, which has leaves that
work as snap-traps . Other kinds of carnivorous plants, such as the sundews,
are decorated with glands that secrete a sticky fluid which both attracts and
then later digests insects that become ensnared in the sticky fluid. And still
another group includes the pitcher plants, which typically catch and hold
rainwater in a pitcher-shaped organ. The plant secretes nutrients as well as
digestive enzymes into the trapped water. Insects are attracted to, and then
fall into, the pool of fluid; they cannot easily escape due to the downward-
facing hairs that line the inside of the "pitcher". One unique kind of pitcher
plant is the California Pitcher Plant (Darlingtonia californica, [link]), found
in bogs and seeps in the mountains of northern California and southern
Oregon. The plant, also known as the Cobra Lily, is unique in that it does
not trap rainwater in the pitcher, but rather pumps it up from the roots. A
tiny entrance hole underneath the "head" of the cobra-shaped structure
allows insects in, but they cannot get back out once they are trapped in the
digestive fluid stored below. All carnivorous plants are found in nitrogen-
poor soils, and obtain the bulk of this critical nutrient from the bodies of
insects and other animals that they trap and digest.
A California Pitcher Plant has
specialized leaves to trap insects.
This specimen was photographed
in the Trinity Alps Wilderness in
northern California. (credit: photo
by D. A. Rintoul)
Photosynthetic Pathways
"You can't have a light without a dark to stick it in"." Arlo Guthrie, American
musician
In a previous module, you learned about photosynthesis, the mechanism plants
use to convert solar energy into chemical energy. The light energy captured is
used to make ATP and NADPH, which is then used to reduce carbon from a
simple form (CO >) into a more complex form (sugars). The first step of the
Calvin cycle is the fixation of carbon dioxide to RuBP, and the plants that only
use this mechanism of carbon fixation are called C3 plants. About 85% of the
plant species on the planet are C3 plants; some examples are rice, wheat,
soybeans and all trees.
The process of photosynthesis has a theoretical efficiency of 30% (i.e., the
maximum amount of chemical energy output would be only 30% of the solar
energy input), but in reality the efficiency is much lower. It is only about 3% on
cloudy days. Why is so much solar energy lost? There are a number of factors
contributing to this energy loss, and one metabolic pathway that contributes to
this low efficiency is photorespiration. During photorespiration, the key
photosynthetic enzyme Rubisco (ribulose-1,5-bisphosphate carboxylase
oxygenase) uses O, as a substrate instead of CO>. This process uses up a
considerable amount of energy without making sugars ([link]). When a plant has
its stomata open (CO; is diffusing in while O> and water are diffusing out),
photorespiration is minimized because Rubisco has a higher affinity for CO
than for O» when air temperatures are below 30°C (86°F). However, when a
plant closes its stomata during times of water stress and O> from photosynthesis
builds up inside the cell, the rate of photorespiration increases because O, is now
more abundant inside the mesophyll. So, there is a tradeoff. Plants can leave the
stomata open and risk drying out, or they can close the stomata, thereby reducing
the uptake of CO», and decreasing the efficiency of photosynthesis. In addition,
Rubisco has a higher affinity for O2 when temperatures increase, which means
that C3 plants use more energy (ATP) for photorespiration at higher
temperatures.
ATP | co, O, ATP
ATP PGA ATP
NADPH NADPH
A comparison of photorespiration and carbon fixation in C3 plants.
During photorespiration, O» is bound to RuBP and forms
phosphoglycolate (PG) and Phosphoglycerate (PGA), PG then
undergoes an number energy requiring reactions releasing CO2. Work
by Eva Horne.
Evolutionarily speaking, why is photorespiration still around? One hypothesis is
that it is evolutionary baggage from a time when the atmosphere had a lower O>
concentration than it does today. In other words, when Rubisco first evolved
millions of years ago, the O» concentration was so low that excluding O, from its
binding site had little or no influence on the efficiency of photosynthesis. The
modern Rubisco retains some of its ancestral affinity for O2, which leads to the
energy costs associated with photorespiration. However, plant cell physiologists
are discovering that there might be some metabolic benefits associated with
photorespiration, which would help explain why this seemingly wasteful
pathway is still found in plants. Adding to the dilemma is the fact that when
plant geneticists “knock out” Rubisco’s ability to fix Oz, Rubisco also loses its
ability to fix COs. It is possible that the active site of this enzyme cannot be
engineered, by artificial or natural selection, so that it exclusively binds CO, and
not Op.
C, plant and CAM Pathways as a Means of Reducing
Photorespiration
The Cy and CAM pathways for fixing CO> are two adaptations that improve the
efficiency of photosynthesis, by ensuring that Rubisco encounters high CO»
concentrations and thus reduces photorespiration. These two photosynthetic
adaptations for fixing CO» have evolved independently a number of times in
species that evolved from wet and dry, but typically warm climates. Why have
these mechanisms evolved independently so many times? Plants that minimize
photorespiration may have a significant competitive advantage, because a
considerable amount of energy (in the form of ATP) is lost in plants during
photorespiration. In many environments, plants that use solar energy more
efficiently should out-compete those which are less efficient.
C, Pathway
In Cy plants, the reactions that fix atmospheric CO, and the Calvin cycle are
physically separated, with the reactions that fix atmospheric CO, occurring in
the mesophyll cells and the Calvin cycle occurring in special cells that surround
the veins in the leaves. These cells are called bundle-sheath cells. How does this
work? Atmospheric CO; is fixed in the mesophyll cells as a simple 4-carbon
organic acid (malate) by an enzyme that has no affinity for O». Malate is then
transported to the bundle-sheath cells. Inside the bundle sheath, malate is
oxidized to a 3-C organic acid, and in the process, 1 molecule of CO; is
produced from every malate molecule ({link]). The CO, is then fixed by Rubisco
into sugars, via the Calvin cycle, exactly as in C3 photosynthesis. There is an
additional cost of two ATPs associated with moving the three-carbon “ferry”
molecule from the bundle sheath cell back to the mesophyll to pick up another
molecule of atmospheric CO>. Since the spatial separation in bundle-sheath cells
minimizes O> concentrations in the locations where Rubisco is located,
photorespiration is minimized ([link]). This arrangement of cells reduces
photorespiration and increases the efficiency of photosynthesis for C, plants. In
addition, Cy plants require about half as much water as a C3 plant. The reason Cy
plants require less water is due to the fact that the physical shape of the stomata
and leaf structure of C, plants helps reduce water loss by developing a large CO»
concentration gradient between the outside of the leaf (400 ppm) and the
mesophyll cells (10 ppm). The large CO» concentration gradient reduces water
loss via transpiration through the stomata.
C; plant C, plant
Stoma Vascular Bundle Mesophyll
tissue sheath cell
cell
Vascular Mesophyll
tissue cell
Stoma
Bundle sheath cell
Cross section of a C3 and Cy, plant leaf. Work by Eva Horne
The spatial separation of Carbon
fixation and the Calvin cycle in C,
plants. Work by Eva Horne
The C4 pathway is used in about 3% of all vascular plants; some examples are
crabgrass, sugarcane and corn. Cy plants are common in habitats that are hot, but
are less abundant in areas that are cooler, because the enzyme that fixes the CO,
in the mesophyll is less efficient at lower temperature. One hypothesis for the
abundance of Cy, plants in hot habitats is that the benefits of reduced
photorespiration and water loss exceeds the ATP cost of moving the the CO)
from the mesophyll cell to bundle-sheath cell.
CAM
Many plants such as cacti and pineapples, which are adapted to arid
environments, use a different energy and water saving pathway called
crassulacean acid metabolism (CAM). This name comes from the family of
plants (Crassulaceae) in which scientists first discovered the pathway. Instead of
separating the light-dependent reactions and the use of CO, in the Calvin cycle
spatially, CAM plants separate these processes temporally ({link]). At night,
CAM plants open their stomata, and an enzyme in the mesophyll cells fix the
CO, as an organic acid and store the organic acid in vacuoles until moming.
During the day the light-dependent reactions supply the ATP and NADPH
necessary for the Calvin cycle to function, and the CO, is released from those
organic acids and used to make sugars. Plant species using CAM photosynthesis
are the most water efficient of all; the stomata are only open at night when
humidity is typically higher and the temperatures are much cooler (which serves
to lower the diffusive gradient driving water loss from leaves). The CAM
pathway is primarily an adaptation to water-limited environments; the fact that
this pathway also stops photorespiration is an added benefit.
Temporal separation of Carbon
fixation and the Calvin cycle in
CAM plants. Work by Eva Horne
Overall, C3, C4 and CAM plants all use the Calvin cycle to make sugars from
CO>. However, the various ways in which plants fix CO, varies with the
advantages and disadvantages associated with the mechanism and the habitats
where plants can be found (Table 1).
As humans continue to burn fossil fuels, CO, levels in the atmosphere will
continue to increase. This human alteration of the environment has sparked the
development of a number of interesting questions. What influence will
increasing CO> have on the distributions of C3, C, and CAM plants? What
influence will increasing CO, have on agricultural production? Is it possible that
an increase in agricultural production by additional CO, in the atmosphere could
offset or mitigate the decrease in agricultural production caused by climate
change?
Cost
Benefits
Separation
of light-
dependent
reactions
and
carbon
fixation
Habitat
C3 plant
Photorespiration
Carbon fixation
without using
ATP
None, all of
these reactions
occur in the
same cells
Cool and moist
C, plant
ATP cost
associated with
fixing carbon
twice. Carbon
fixation is less
efficient under
cold conditions.
Reduced
photorespiration
and ability to
fix Carbon
under high
temperatures
and reduced
water loss
Spatial, these
two sets of
reactions occur
in different cells
Hot, not in cold
environments
(see cost.)
CAM Plant
Reduced
amount of fixed
carbon, stomata
only open at
night
Reduced
photorespiration
and reduced
water loss
Temporal, these
two sets of
reactions occur
at different
times of day
Hot and dry,
large
temperature
differential
between night
and day
Characteristics of C3, Cz and CAM methods of fixing CO,
Climate and the Effects of Global Climate Change
""Every year, by burning fossil fuels, we release a million years of
photosynthesis" Daniel Nocera, an MIT scientist working to develop a
process which uses sunlight and water to produce energy, quoted in "The
Artificial Leaf" by Daniel Owen, The New Yorker, May 14, 2012.
All biomes are affected by global conditions, such as climate, that
ultimately shape each biome’s environment. Scientists who study climate
have noted a series of marked changes that have gradually become
increasingly evident during the last sixty years. Global climate change is
the term used to describe altered global weather patterns, including a
worldwide increase in temperature, due largely to rising levels of
atmospheric carbon dioxide.
Climate and Weather
A common misconception about global climate change is that a specific
weather event occurring in a particular region (for example, a very cool
week in June in central Indiana) is evidence of global climate change.
However, a cold week in June is a weather-related event and not a climate-
related one. These misconceptions often arise because of confusion over the
terms climate and weather.
Climate refers to the long-term, predictable atmospheric conditions of a
specific area. The climate of a biome is characterized by having consistent
temperature and annual rainfall ranges. Climate does not address the
amount of rain that fell on one particular day in a biome or the colder-than-
average temperatures that occurred on one day. In contrast, weather refers
to the conditions of the atmosphere during a short period of time. Weather
forecasts are usually made for 48-hour cycles. Long-range weather
forecasts are available but can be unreliable.
To better understand the difference between climate and weather, imagine
that you are planning an outdoor event in northern Wisconsin. You would
be thinking about climate when you plan the event in the summer rather
than the winter because you have long-term knowledge that any given
Saturday in the months of May to August would be a better choice for an
outdoor event in Wisconsin than any given Saturday in January. However,
you cannot determine the specific day that the event should be held on
because it is difficult to accurately predict the weather on a specific day.
Climate can be considered “average” weather.
Global Climate Change
Climate change can be understood by approaching three areas of study:
¢ current and past global climate change
¢ causes of past and present-day global climate change
¢ ancient and current results of climate change
It is helpful to keep these three different aspects of climate change clearly
separated when consuming media reports about global climate change. It is
common for reports and discussions about global climate change to confuse
the data showing that Earth’s climate is changing with the factors that drive
this climate change.
Evidence for Global Climate Change
Since scientists cannot go back in time to directly measure climatic
variables, such as average temperature and precipitation, they must instead
indirectly measure temperature. To do this, scientists rely on historical
evidence of Earth’s past climate.
Antarctic ice cores are a key example of such evidence. These ice cores are
samples of polar ice obtained by means of drills that reach thousands of
meters into ice sheets or high mountain glaciers. Viewing the ice cores is
like traveling backwards through time; the deeper the sample, the earlier the
time period. Trapped within the ice are bubbles of air and other biological
evidence that can reveal temperature and carbon dioxide data. Antarctic ice
cores have been collected and analyzed to indirectly estimate the
temperature of the Earth over the past 400,000 years ([link]a). The 0 °C on
this graph refers to the long-term average. Temperatures that are greater
than 0 °C exceed Earth’s long-term average temperature. Conversely,
temperatures that are less than 0 °C are less than Earth’s average
temperature. This figure shows that there have been periodic cycles of
increasing and decreasing temperature.
Before the late 1800s, the Earth has been as much as 9 °C cooler and about
3 °C warmer. Note that the graph in [link]b shows that the atmospheric
concentration of carbon dioxide has also risen and fallen in periodic cycles;
note the relationship between carbon dioxide concentration and
temperature. [link ]b shows that carbon dioxide levels in the atmosphere
have historically cycled between 180 and 300 parts per million (ppm) by
volume.
Ls]
“i
ua
S
a
CO, concentration (ppm)
N
3
8
~~
ua
Ice at the Russian Vostok station
in East Antarctica was laid down
over the course 420,000 years and
reached a depth of over 3,000 m.
By measuring the amount of CO»
trapped in the ice, scientists have
determined past atmospheric CO>
concentrations. Temperatures
relative to modern day were
determined from the amount of
deuterium (an isotope of
hydrogen) present.
[link]a does not show the last 2,000 years with enough detail to compare
the changes of Earth’s temperature during the last 400,000 years with the
temperature change that has occurred in the more recent past. Two
significant temperature anomalies, or irregularities, have occurred in the last
2000 years. These are the Medieval Climate Anomaly (or the Medieval
Warm Period) and the Little Ice Age. A third temperature anomaly aligns
with the Industrial Era. The Medieval Climate Anomaly occurred between
900 and 1300 AD. During this time period, many climate scientists think
that slightly warmer weather conditions prevailed in many parts of the
world; the higher-than-average temperature changes varied between 0.10 °C
and 0.20 °C above the norm. Although 0.10 °C does not seem large enough
to produce any noticeable change, it did free seas of ice. Because of this
warming, the Vikings were able to colonize Greenland.
The Little Ice Age was a cold period that occurred between 1550 AD and
1850 AD. During this time, a slight cooling of a little less than 1 °C was
observed in North America, Europe, and possibly other areas of the Earth.
This 1 °C change in global temperature is a seemingly small deviation in
temperature (as was observed during the Medieval Climate Anomaly);
however, it also resulted in noticeable changes. Historical accounts reveal a
time of exceptionally harsh winters with much snow and frost.
The Industrial Revolution, which began around 1750, was characterized by
changes in much of human society. Advances in agriculture increased the
food supply, which improved the standard of living for people in Europe
and the United States. New technologies were invented and provided jobs
and cheaper goods. These new technologies were powered using fossil
fuels, especially coal. The Industrial Revolution starting in the early
nineteenth century ushered in the beginning of the Industrial Era. When a
fossil fuel is burned, carbon dioxide is released. With the beginning of the
Industrial Era, atmospheric carbon dioxide began to rise ([link]).
Atmospheric CO, at Mauna Loa Observatory
400
Scripps Institution of Oceanography
NOAA Earth System Research Laboratory
380
360
340
PARTS PER MILLION
320
March 2014
1960 1970 1980 1990 2000 2010
YEAR
The atmospheric concentration of CO, has risen steadily since the
beginning of industrialization. Graph from
http://www.esrl.noaa.gov/gmd/webdata/ccg¢g/trends/co2_data_mlo.pdf
Current and Past Drivers of Global Climate Change
Scientists also use indirect evidence to determine the drivers, or factors, that
may be responsible for climate change. The indirect evidence includes data
collected using ice cores, boreholes (a narrow shaft bored into the ground),
tree rings, glacier lengths, pollen remains, and ocean sediments. The data
shows a correlation between the timing of temperature changes and drivers
of climate change: before the Industrial Era (pre-1780), there were three
drivers of climate change that were not related to human activity or
atmospheric gases. The first of these is the Milankovitch cycles. The
Milankovitch cycles describe the effects of slight changes in the Earth’s
orbit on Earth’s climate. The length of the Milankovitch cycles ranges
between 19,000 and 100,000 years. In other words, one could expect to see
some predictable changes in the Earth’s climate associated with changes in
the Earth’s orbit at a minimum of every 19,000 years.
The variation in the sun’s intensity is the second natural factor responsible
for climate change. Solar intensity is the amount of solar power or energy
the sun emits in a given amount of time. There is a direct relationship
between solar intensity and temperature. As solar intensity increases (or
decreases), the Earth’s temperature correspondingly increases (or
decreases). Changes in solar intensity have been proposed as one of several
possible explanations for the Little Ice Age.
Finally, volcanic eruptions are a third natural driver of climate change.
Volcanic eruptions can last a few days, but the solids and gases released
during an eruption can influence the climate over a period of a few years,
causing short-term climate changes. The gases and solids released by
volcanic eruptions can include carbon dioxide, water vapor, sulfur dioxide,
hydrogen sulfide, hydrogen, and carbon monoxide. Generally, volcanic
eruptions cool the climate. This occurred in 1783 when volcanos in Iceland
erupted and caused the release of large volumes of sulfuric oxide. This led
to haze-effect cooling, a global phenomenon that occurs when dust, ash, or
other suspended particles block out sunlight and trigger lower global
temperatures as a result; haze-effect cooling usually extends for one or
more years. In Europe and North America, haze-effect cooling produced
some of the lowest average winter temperatures on record in 1783 and
1784.
Greenhouse gases are probably the most significant drivers of the climate.
When heat energy from the sun strikes the Earth, gases known as
greenhouse gases trap the heat in the atmosphere, as do the glass panes of a
greenhouse keep heat from escaping. The greenhouse gases that affect Earth
include carbon dioxide, methane, water vapor, nitrous oxide, and ozone.
Approximately half of the radiation from the sun passes through these gases
in the atmosphere and strikes the Earth. This radiation is converted into
thermal radiation on the Earth’s surface, and then a portion of that energy is
re-radiated back into the atmosphere. Greenhouse gases, however, reflect
much of the thermal energy back to the Earth’s surface. The more
greenhouse gases there are in the atmosphere, the more thermal energy is
reflected back to the Earth’s surface. Greenhouse gases absorb and emit
radiation and are an important factor in the greenhouse effect: the warming
of Earth due to carbon dioxide and other greenhouse gases in the
atmosphere.
Evidence supports the relationship between atmospheric concentrations of
carbon dioxide and temperature: as carbon dioxide rises, global temperature
rises. Since 1950, the concentration of atmospheric carbon dioxide has
increased from about 280 ppm to 382 ppm in 2006. In 2013, the
atmospheric carbon dioxide concentration was 400 ppm.
Scientists look at patterns in data and try to explain differences or
deviations from these patterns. The atmospheric carbon dioxide data reveal
a historical pattern of carbon dioxide increasing and decreasing, cycling
between a low of 180 ppm and a high of 300 ppm. Scientists have
concluded that it took around 50,000 years for the atmospheric carbon
dioxide level to increase from its low minimum concentration to its higher
maximum concentration. However, starting recently, atmospheric carbon
dioxide concentrations have increased beyond the historical maximum of
300 ppm. The current increases in atmospheric carbon dioxide have
happened very quickly—in a matter of hundreds of years rather than
thousands of years. What is the reason for this difference in the rate of
change and the amount of increase in carbon dioxide? A key factor that
must be recognized when comparing the historical data and the current data
is the presence of modern human society; no other driver of climate change
has yielded changes in atmospheric carbon dioxide levels at this rate or to
this magnitude.
Human activity releases carbon dioxide and methane, two of the most
important greenhouse gases, into the atmosphere in several ways. The
primary mechanism that releases carbon dioxide is the burning of fossil
fuels, such as gasoline, coal, and natural gas ([{link]). Deforestation, cement
manufacture, animal agriculture, the clearing of land, and the burning of
forests are other human activities that release carbon dioxide. Methane
(CH,) is produced when bacteria break down organic matter under
anaerobic conditions. Anaerobic conditions can happen when organic
matter is trapped underwater (such as in rice paddies) or in the intestines of
herbivores. Methane can also be released from natural gas fields and the
decomposition that occurs in landfills. Another source of methane is the
melting of clathrates. Clathrates are frozen chunks of ice and methane
found at the bottom of the ocean. When water warms, these chunks of ice
melt and methane is released. As the ocean’s water temperature increases,
the rate at which clathrates melt is increasing, releasing even more methane.
This leads to increased levels of methane in the atmosphere, which further
accelerates the rate of global warming. This is an example of the positive
feedback loop that is leading to the rapid rate of increase of global
temperatures.
The burning of fossil
fuels in industry and by
vehicles releases carbon
dioxide and other
greenhouse gases into the
atmosphere. (credit:
“P6oll6”/Wikimedia
Commons)
Documented Results of Climate Change: Past and Present
Scientists have geological evidence of the consequences of long-ago
climate change. Modern-day phenomena such as retreating glaciers and
melting polar ice cause a continual rise in sea level. Meanwhile, changes in
climate can negatively affect organisms.
Past Climate Change
Global warming has been associated with at least one planet-wide
extinction event during the geological past. The Permian extinction event
occurred about 251 million years ago toward the end of the roughly 50-
million-year-long geological time span known as the Permian period. This
geologic time period was one of the three warmest periods in Earth’s
geologic history. Scientists estimate that approximately 70 percent of the
terrestrial plant and animal species and 84 percent of marine species
became extinct, vanishing forever near the end of the Permian period.
Organisms that had adapted to wet and warm climatic conditions, such as
annual rainfall of 300-400 cm (118-157 in) and 20 °C—30 °C (68 °F-86 °F)
in the tropical wet forest, may not have been able to survive the Permian
climate change.
Present Climate Change
A number of global events have occurred that may be attributed to climate
change during our lifetimes. Glacier National Park in Montana is
undergoing the retreat of many of its glaciers, a phenomenon known as
glacier recession. In 1850, the area contained approximately 150 glaciers.
By 2010, however, the park contained only about 24 glaciers greater than
25 acres in size. One of these glaciers is the Grinnell Glacier ({link]) at
Mount Gould. Between 1966 and 2005, the size of Grinnell Glacier shrank
by 40 percent. Similarly, the mass of the ice sheets in Greenland and the
Antarctic is decreasing: Greenland lost 150-250 km? of ice per year
between 2002 and 2006. In addition, the size and thickness of the Arctic sea
ice is decreasing.
The effect of global warming can be seen in the continuing
retreat of Grinnel Glacier. The mean annual temperature in the
park has increased 1.33 °C since 1900. The loss of a glacier
results in the loss of summer meltwaters, sharply reducing
seasonal water supplies and severely affecting local
ecosystems. (credit: modification of work by USGS)
This loss of ice is leading to increases in the global sea level. On average,
the sea is rising at a rate of 1.8 mm per year. However, between 1993 and
2010 the rate of sea level increase ranged between 2.9 and 3.4 mm per year.
A variety of factors affect the volume of water in the ocean, including the
temperature of the water (the density of water is related to its temperature)
and the amount of water found in rivers, lakes, glaciers, polar ice caps, and
sea ice. As glaciers and polar ice caps melt, there is a significant
contribution of liquid water that was previously frozen.
In addition to some abiotic conditions changing in response to climate
change, many organisms are also being affected by the changes in
temperature. Temperature and precipitation play key roles in determining
the geographic distribution and phenology of plants and animals.
(Phenology is the study of the effects of climatic conditions on the timing of
periodic lifecycle events, such as flowering in plants or migration in birds.)
Researchers have shown that 385 plant species in Great Britain are
flowering 4.5 days sooner than was recorded earlier during the previous 40
years. In addition, insect-pollinated species were more likely to flower
earlier than wind-pollinated species. The impact of changes in flowering
date would be mitigated if the insect pollinators emerged earlier. This
mismatched timing of plants and pollinators could result in injurious
ecosystem effects because, for continued survival, insect-pollinated plants
must flower when their pollinators are present.
Human Population Continues to Grow
Introduction
"Population, when unchecked, increases in a geometrical ratio. Subsistence
increases only in an arithmetical ratio. A slight acquaintance with numbers
will show the immensity of the first power in comparison of the second."
Thomas Robert Malthus. An Essay on the Principle of Population, (1798)
Mathematical approaches to understanding animal population dynamics,
which you learned about earlier in the semester, can be applied to human
population growth. Malthus recognized long ago that exponential
population growth might be a problem if resources increase non-
exponentially. Resources can be increased by technology and other
modifications to the environment. In fact, humans are not unique in their
ability to alter their environment. For example, beaver dams alter the stream
environment where they are built. Humans, however, have the ability to
alter their environment to increase its carrying capacity sometimes to the
detriment of other species (e.g., via artificial selection for crops that have a
higher yield). Earth’s human population is growing rapidly, to the extent
that some worry about the ability of the earth’s environment to sustain this
population, as long-term exponential growth carries the potential risks of
famine, disease, and large-scale death.
Although humans have increased the carrying capacity of their
environment, the technologies used to achieve this transformation have
caused unprecedented changes to Earth’s environment, altering ecosystems
to the point where some may be in danger of collapse. The depletion of the
ozone layer, erosion due to acid rain, and damage from global climate
change are caused by human activities. The ultimate effect of these changes
on our carrying capacity is unknown. As some point out, it is likely that the
negative effects of increasing carrying capacity will outweigh the positive
ones—the carrying capacity of the world for human beings might actually
decrease.
The world’s human population is currently experiencing exponential growth
even though human reproduction is far below its biotic potential ((link]). To
reach its biotic potential, all females would have to become pregnant every
nine months or so during their reproductive years. Also, resources would
have to be such that the environment would support such growth. Neither of
these two conditions exists. In spite of this fact, human population is still
growing exponentially.
— World
== Africa
_ == Asia
~~ Europe
3,000,000 = Latin America
== Northern America
5,000,000
-
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Human population growth since 1000 AD is
exponential (dark blue line). Notice that while
the population in Asia (yellow line), which has
many economically underdeveloped countries,
is increasing exponentially, the population in
Europe (light blue line), where most of the
countries are economically developed, is
growing much more slowly.
A consequence of exponential human population growth is the time that it
takes to add a particular number of humans to the Earth is becoming
shorter. [link] shows that 123 years were necessary to add 1 billion humans
in 1930, but it only took 24 years to add two billion people between 1975
and 1999. As already discussed, at some point it would appear that our
ability to increase our carrying capacity indefinitely on a finite world is
uncertain. Without new technological advances, the human growth rate has
been predicted to slow in the coming decades. However, the population will
still be increasing and the threat of overpopulation remains.
Time between Billions in World Population Growth
1 billion: 1800
2 billion: 1930
3 billion: 1960
4 billion: 1975
5 billion: 1987
6 billion: 1999
7 billion: 2012
8 billion: 2028
9 billion: 2054
Years
Source: Population Reference Bureau
The time between the addition of each billion human
beings to Earth decreases over time. (credit:
modification of work by Ryan T. Cragun)
Overcoming Density-Dependent Regulation
Humans are unique in their ability to alter their environment with the
conscious purpose of increasing its carrying capacity. This ability is a major
factor responsible for human population growth and a way of overcoming
density-dependent growth regulation. Much of this ability is related to
human intelligence, society, and communication. Humans can construct
shelter to protect them from the elements and have developed agriculture
and domesticated animals to increase their food supplies. In addition,
humans use language to communicate this technology to new generations,
allowing them to improve upon previous accomplishments.
Other factors in human population growth are migration and public health.
Humans originated in Africa, but have since migrated to nearly all
inhabitable land on the Earth. Public health, sanitation, and the use of
antibiotics and vaccines have decreased the ability of infectious disease to
limit human population growth. In the past, diseases such as the bubonic
plaque of the fourteenth century killed between 30 and 60 percent of
Europe’s population and reduced the overall world population by as many
as 100 million people. Today, the threat of infectious disease, while not
gone, is certainly less severe. According to the World Health Organization,
global death from infectious disease declined from 14.2 million in 2000 to
9.9 million in 2011. To compare to some of the epidemics of the past, the
percentage of the world's population killed between 1993 and 2002
decreased from 0.30 percent of the world's population to 0.24 percent. Thus,
it appears that the influence of infectious disease on human population
growth is becoming less significant.
Long-Term Consequences of Exponential Human Population
Growth
Many dire predictions have been made about the world’s population leading
to a major crisis called the “population explosion.” In the 1968 book The
Population Bomb, biologist Dr. Paul R. Ehrlich wrote, “The battle to feed
all of humanity is over. In the 1970s hundreds of millions of people will
Starve to death in spite of any crash programs embarked upon now. At this
late date nothing can prevent a substantial increase in the world death
rate,” footnote] While many critics view this statement as an exaggeration, the
laws of exponential population growth are still in effect, and unchecked
human population growth cannot continue indefinitely.
Paul R. Erlich, prologue to The Population Bomb, (1968; repr., New York:
Ballantine, 1970).
Efforts to control population growth led to the one-child policy in China,
which used to include more severe consequences, but now imposes fines on
urban couples who have more than one child. Due to the fact that some
couples wish to have a male heir, many Chinese couples continue to have
more than one child. The policy itself, its social impacts, and the
effectiveness of limiting overall population growth are controversial. In
spite of population control policies, the human population continues to
grow. At some point the food supply may run out because of the subsequent
need to produce more and more food to feed our population. The United
Nations estimates that future world population growth may vary from 6
billion (a decrease) to 16 billion people by the year 2100. There is no way
to know whether human population growth will moderate to the point
where the crisis described by Dr. Ehrlich will be averted.
Another result of population growth is the endangerment of the natural
environment. Many countries have attempted to reduce the human impact
on climate change by reducing their emission of the greenhouse gas carbon
dioxide. However, these treaties have not been ratified by every country,
and many underdeveloped countries trying to improve their economic
condition may be less likely to agree with such provisions if it means
slower economic development. Furthermore, the role of human activity in
causing climate change has become a hotly debated socio-political issue in
some developed countries, including the United States. Thus, we enter the
future with considerable uncertainty about our ability to curb human
population growth and protect our environment.
Features of the Animal Kingdom
Introduction
"Stones grow; plants grow and live; animals grow, live and feel." Linneaus,
in Philosophia Botanica, 1751
The differences between the animal, vegetable and mineral classes are a bit
more complicated than the simple scheme of Linneaus. Members of the
animal kingdom are incredibly diverse, but all animals share common
features that distinguish them from organisms in other kingdoms. All
animals are eukaryotic, multicellular organisms, and almost all animals
have specialized tissues. All animals are motile, at least during certain life
stages. Animals require a source of food to grow and develop. All animals
are heterotrophic, ingesting living or dead organic matter. This form of
obtaining energy distinguishes them from autotrophic organisms, such as
most plants, which make their own nutrients through photosynthesis and
from fungi that digest their food externally. Animals may be carnivores,
herbivores, omnivores, or parasites ([link]). Most animals reproduce
sexually: The offspring pass through a series of developmental stages that
establish a determined body plan, unlike plants, for example, in which the
exact shape of the body is indeterminate. The body plan refers to the shape
of an animal.
(a)
All animals that derive energy from food are heterotrophs. The
(a) black bear is an omnivore, eating both plants and animals.
The (b) heartworm Dirofilaria immitis is a parasite that derives
energy from its hosts. It spends its larval stage in mosquitos
and its adult stage infesting the hearts of dogs and other
mammals, as shown here. (credit a: modification of work by
USDA Forest Service; credit b: modification of work by Clyde
Robinson)
Complex Tissue Structure
A hallmark trait of animals is specialized structures that are differentiated to
perform unique functions. As multicellular organisms, most animals
develop specialized cells that group together into tissues with specialized
functions. A tissue is a collection of similar cells that had a common
embryonic origin that share a specialized function. There are four main
types of animal tissues: nervous, muscle, connective, and epithelial.
e Nervous tissue contains neurons, or nerve cells, which transmit nerve
impulses.
e Muscle tissue contracts to cause all types of body movement from
locomotion of the organism to movements within the body itself. You
will learn more about the diferent types of muscle tissue later in this
unit.
e Animals also have specialized connective tissues that provide many
functions, including transport and structural support. Examples of
connective tissues include blood and bone. Connective tissue is
comprised of cells separated by extracellular material made of organic
and inorganic materials, such as the protein and mineral deposits of
bone.
e Epithelial tissue covers the internal and external surfaces of organs
inside the animal body and the external surface of the body of the
organism.
Animal Reproduction and Development
Most animals have diploid body (somatic) cells and a small number of
haploid reproductive (gamete) cells produced through meiosis. Some
exceptions exist: For example, in bees, wasps, and ants, the male is haploid
because it develops from an unfertilized egg. Most animals undergo sexual
reproduction, while many also have mechanisms of asexual reproduction.
Asexual Reproduction
Asexual reproduction, unlike sexual reproduction, produces offspring
genetically identical to each other and to the parent. A number of animal
species—especially those without backbones, but even some fish,
amphibians, and reptiles—are capable of asexual reproduction. Asexual
reproduction, except for occasional identical twinning, is absent in birds
and mammals. The most common forms of asexual reproduction for
stationary aquatic animals include budding and fragmentation, in which part
of a parent individual can separate and grow into a new individual. In
contrast, a form of asexual reproduction found in certain invertebrates and
rare vertebrates is called parthenogenesis (or “virgin beginning”), in which
unfertilized eggs develop into new offspring.
Sexual Reproduction and Embryonic Development
Almost all animal species are capable of reproducing sexually; for many,
this is the only mode of reproduction possible. This distinguishes animals
from fungi, protists, and bacteria, where asexual reproduction is common or
exclusive. During sexual reproduction, the male and female gametes of a
species combine in a process called fertilization. Typically, the small, motile
male sperm travels to the much larger, sessile female egg. Sperm form is
diverse and includes cells with flagella or amoeboid cells to facilitate
motility. Fertilization and fusion of the gamete nuclei produce a zygote.
Fertilization may be internal, especially in land animals, or external, as is
common in many aquatic species.
After fertilization, a developmental sequence ensues as cells divide and
differentiate. Many of the events in development are shared in groups of
related animal species, and these events are one of the main ways scientists
classify high-level groups of animals. During development, animal cells
specialize and form tissues, determining their future morphology and
physiology. In many animals, such as mammals, the young resemble the
adult. Other animals, such as some insects and amphibians, undergo
complete metamorphosis in which individuals enter one or more larval
stages. For these animals, the young and the adult have different diets and
sometimes habitats. In other species, a process of incomplete
metamorphosis occurs in which the young somewhat resemble the adults
and go through a series of stages separated by molts (shedding of the skin)
until they reach the final adult form.
Features used in the Classification of Animals
Animals are classified according to morphological and developmental
characteristics, such as a body plan. With the exception of sponges, the
animal body plan is symmetrical. This means that their distribution of body
parts is balanced along an axis. Additional characteristics that contribute to
animal classification include the number of tissue layers formed during
development, the presence or absence of an internal body cavity, and other
features of embryological development.
Arthropods
Ecdysozoa
Protostomia
Bilateria
(bilateral
symmetry,
triploblastic)
Eumetazoa
(specialized
tissues)
Lophotrochozoa
Metazoa Deuterostomia
(animals)
Radiata
(radial symmetry, diploblastic)
Parazoa (no tissues)
The phylogenetic tree of animals is based on
morphological, fossil, and genetic evidence.
Body Symmetry
Animals may be asymmetrical, radial, or bilateral in form ([link]).
Asymmetrical animals are animals with no pattern or symmetry; an
example of an asymmetrical animal is a sponge ([link]a). An organism with
radial symmetry ((link]b) has a longitudinal (up-and-down) orientation:
Any plane cut along this up—down axis produces roughly mirror-image
halves. An example of an organism with radial symmetry is a sea anemone.
Dorsal =
| Posterior
Asymmetry Radial symmetry Bilateral symmetry
(a) (b) (c)
Animals exhibit different types of body symmetry. The (a)
sponge is asymmetrical and has no planes of symmetry, the (b)
sea anemone has radial symmetry with multiple planes of
symmetry, and the (c) goat has bilateral symmetry with one
plane of symmetry.
Bilateral symmetry is illustrated in [link]c using a goat. The goat also has
upper and lower sides to it, but they are not symmetrical. A vertical plane
cut from front to back separates the animal into roughly mirror-image right
and left sides. Animals with bilateral symmetry also have a “head” and
“tail” (anterior versus posterior) and a back and underside (dorsal versus
ventral).
Getting a Head
A product of bilateral symmetry and of organisms having a head (anterior)
and a tail (posterior) is the fact organisms move through their environment
head first. Since organisms move through their environment head first, a
significant advantage can be seen with organisms that have a concentration
of sensory organs in the head region or cephalization. In other words,
placement of sensory organs around the mouth of a heterotroph allows it to
be more efficient at finding food. In addition, organisms moving around
with the sensory organs in the front will be more efficient at detecting
potential predators and not becoming food.
Segmentation
The division of an animal into repeating body parts is called segmentation.
You can clearly see segmentation in earthworms and millipeds, but in some
insects and chordates the subdivisions are not as obvious. What are the
advantages of a segmented body? Segmentation allows for greater
flexibility and mobility. The repeating body parts allows for specialization
of specific body parts, such as the development of legs, arm and wings.
Germ Layers
Nearly all animal species undergo a layering of early tissues during
embryonic development. These layers are called germ layers. Each layer
develops into a specific set of tissues and organs. Animals develop either
two or three embryonic germ layers ({link]). The animals that display radial
symmetry develop two germ layers, an inner layer (endoderm) and an outer
layer (ectoderm). These animals are called diploblasts. Animals with
bilateral symmetry develop three germ layers: an inner layer (endoderm), an
outer layer (ectoderm), and a middle layer (mesoderm). Animals with three
germ layers are called triploblasts.
Diploblast Triploblast
Endoderm
Digestive
Cavity
f+ Ectoderm
Non-living layer Mesoderm
During embryogenesis, diploblasts
develop two embryonic germ layers: an
ectoderm and an endoderm. Triploblasts
develop a third layer—the mesoderm—
between the endoderm and ectoderm.
In triploblasts, the three germ layers develop in all the parts of an adult
animal. The endoderm gives rise to the innermost lining of internal organs,
such as those in the digestive tract, the liver, the pancreas and the lining of
the lungs. The majority of organs and tissues in an adult animal such as the
kidney, heart, muscles, blood vessels, bones and the dermis (inner layer of
skin) develop from the mesoderm. Lastly, the ectoderm develops into the
outermost layer of skin (epidermis), the lens and cornea of the eye, and the
nervous system (brain and nerves).
Germ
Layer
Ectoderm
Mesoderm
Endoderm
Tissue types
Outer layer of skin, nerves, brain, cornea and lens of
the eye
Connective tissue of skin (dermis), bone, muscle
(including cardiac muscle), cartilage, blood cells and
blood vessels, fat cells, reproductive tract
Internal lining of organs of the digestive tract, internal
lining of respiratory tract, liver
Examples of tissue types that come from the three germ layers
Presence or Absence of a Coelom
Triploblasts may develop an internal body cavity lined with cells derived
from mesoderm, called a coelom (pr. see-LOM). This epithelial-lined cavity
is a space, usually filled with fluid, which lies between the digestive system
and the body wall. It houses organs such as the kidneys and spleen, and
contains the circulatory system. An Organ is a differentiated structure that
performs a specific function in an organism; it consists of many cells and of
various tissue types. Triploblasts that do not develop a coelom are called
acoelomates, and this internal region is completely filled with tissue,
although they have a gut cavity. Examples of acoelomates include the
flatworms. Animals with a true coelom are called eucoelomates (or
coelomates) ([link]). A true coelom arises entirely within the mesoderm
germ layer. Animals such as earthworms, snails, insects, starfish, and
vertebrates are all eucoelomates. A third group of triploblasts has a body
cavity that is derived partly from mesoderm and partly from endoderm
tissue. These animals are called pseudocoelomates. Roundworms are
examples of pseudocoelomates. New data on the relationships of
pseudocoelomates suggest that these phyla are not closely related and so the
evolution of the pseudocoelom must have occurred more than once ([link]).
True coelomates can be further characterized based on features of their
early embryological development.
Flatworm: Pseudobiceros bedfordi Annelid: Glycera Nematode: Heterodera glycines
Pseudocoelom
Digestive cavity
Ectoderm
Coelom
Mesoderm
Endoderm
Mesoderm
Digestive cavity Endoderm Ectoderm
(a) Acoelomate (b) Eucoelomate (c) Pseudocoelomate
(flatworms) (annelids, (roundworms)
mollusks,
arthropods,
echinoderms,
chordates)
Triploblasts may be acoelomates, eucoelomates, or
pseudocoelomates. Eucoelomates have a body cavity within the
mesoderm, called a coelom, which is lined with mesoderm
tissue. Pseudocoelomates have a similar body cavity, but it is
lined with mesoderm and endoderm tissue. (credit a:
modification of work by Jan Derk; credit b: modification of
work by NOAA; credit c: modification of work by USDA,
ARS)
Protostomes and Deuterostomes
Bilaterally symmetrical, triploblastic eucoelomates can be divided into two
groups based on differences in their early embryonic development. You
may have noticed in [link] the terms "Protostomia" and "Deuterostomia".
Protostomes (members of the Protostomia) include phyla such as
arthropods, mollusks, and annelids. Deuterostomes (members of the
Deuterostomia) include the chordates and echinoderms. These two groups
are named from which opening of the digestive cavity develops first: mouth
or anus. The word protostome comes from Greek words meaning “mouth
first,” and deuterostome originates from words meaning “mouth second” (in
this case, the anus develops first). This difference reflects the fate of a
structure called the blastopore ({link]), which becomes the mouth in
protostomes and the anus in deuterostomes. There are other developmental
differences between protostomes and deuterostomes, including the mode of
formation of the coelom and the pattern of early cell division of the embryo.
Protostomes Deuterostomes
G
Blastopore
Coelom
I Developing
Mesoderm
Mouth coelom
Anus
Digestive
tube
Anus Mouth
Eucoelomates can be divided into two
groups, protostomes and
deuterostomes, based on their early
embryonic development. Two of these
differences include the origin of the
mouth opening and the way in which
the coelom is formed.
Animal Tissue Types
Introduction
" The elementary parts of all tissues are formed of cells in an analogous,
though very diversified manner, so that it may be asserted, that there is one
universal principle of development for the elementary parts of organisms,
however different, and that this principle is the formation of cells." Theodor
Schwann, in Microscopic Researches into the Accordance in the Structure
and Growth of Animals and Plants, 1839
Cells make tissues, tissues make organs, and organs make organ systems.
The tissues of multicellular, complex animals are four primary types:
epithelial, connective, muscle, and nervous. Recall that tissues are groups of
similar cells carrying out a specific related functions. Many different tissues
combine to form an organ—like the skin or kidney—that have specialized
functions within the body. Organs are organized into organ systems to
perform functions; examples include the circulatory system, which consists
of the heart and blood vessels, and the digestive system, consisting of
several organs, including the stomach, intestines, liver, and pancreas. Organ
systems come together to create an entire organism.
Epithelial Tissues
Epithelial tissues cover the outside of organs and structures in the body and
line the lumens of organs in a single layer or multiple layers of cells. The
types of epithelia are classified by the shapes of cells present and the
number of layers of cells. Epithelia composed of a single layer of cells is
called simple epithelia; epithelial tissue composed of multiple layers is
called stratified epithelia. [link] summarizes the different types of
epithelial tissues.
Different Types of Epithelial Tissues
Diiifesieapal ypes DEscpiplanlial Tissues Location
Cell shape Description Location
flat, irregular round simple: lung alveoli,
squamous capillaries stratified:
shape
skin, mouth, vagina
. h ntral
cuboidal cube shaped, centra glands, renal tubules
nucleus
tall, narrow, nucleus simple: digestive tract
columnar toward base tall, narrow, pseudostratified:
nucleus along cell respiratory tract
nd, simpl :
transitional rouge, ot aple uu urinary bladder
appear stratified
Squamous Epithelia
Squamous epithelial cells are generally round, flat, and have a small,
centrally located nucleus. The cell outline is slightly irregular, and cells fit
together to form a covering or lining. When the cells are arranged in a
single layer (simple epithelia), they facilitate diffusion in tissues, such as
the areas of gas exchange in the lungs and the exchange of nutrients and
waste at blood capillaries.
Squamous epithelia cells (a) have a slightly irregular
shape, and a small, centrally located nucleus. These
cells can be stratified into layers, as in (b) this human
cervix specimen. (credit b: modification of work by
Ed Uthman; scale-bar data from Matt Russell)
[link]a illustrates a layer of squamous cells with their membranes joined
together to form an epithelium. Image [link]b illustrates squamous
epithelial cells arranged in stratified layers, where protection is needed on
the body from outside abrasion and damage. This is called a stratified
squamous epithelium and occurs in the skin and in tissues lining the mouth
and vagina.
Cuboidal Epithelia
Cuboidal epithelial cells, shown in [link], are cube-shaped with a single,
central nucleus. They are most commonly found in a single layer
representing a simple epithelia in glandular tissues (e.g. pancreas,
mammary gland, etc.). They are also found in the walls of tubules and in the
ducts of the kidney and liver.
Simple cuboidal
epithelial cells line
tubules in the
mammalian kidney,
where they are involved
in filtering the blood.
Columnar Epithelia
Columnar epithelial cells are taller than they are wide: they resemble a
stack of columns in an epithelial layer, and are most commonly found in a
single-layer arrangement. The nuclei of columnar epithelial cells in the
digestive tract appear to be lined up at the base of the cells, as illustrated in
[link]. These cells absorb material from the lumen of the digestive tract and
prepare it for entry into the body through the circulatory and lymphatic
systems.
Goblet cells
= Columnar = =
eau. epithelial cells ean a
Simple columnar epithelial cells
absorb material from the
digestive tract. Goblet cells
secret mucous into the digestive
tract lumen (at top of the
figure).
Columnar epithelial cells lining the respiratory tract appear to be stratified.
However, each cell is attached to the base membrane of the tissue and,
therefore, they are simple tissues. The nuclei are arranged at different levels
in the layer of cells, making it appear as though there is more than one
layer, as seen in [link]. This is called pseudostratified, columnar epithelia.
This cellular covering has cilia at the apical, or free, surface of the cells.
The cilia enhance the movement of mucous and trapped particles out of the
respiratory tract, helping to protect the system from invasive
microorganisms and harmful material that has been breathed into the body.
Goblet cells are interspersed in some tissues (such as the lining of the
trachea). The goblet cells contain mucous that traps irritants, which in the
case of the trachea keep these irritants from getting into the lungs.
Goblet cells
<a
mm PSeudostratified — c~
epithelial cells
Pseudostratified columnar
epithelia line the
respiratory tract. They
exist in one layer, but the
arrangement of nuclei at
different levels makes it
appear that there is more
than one layer. Goblet
cells interspersed between
the columnar epithelial
cells secrete mucous into
the respiratory tract (at
top of the figure).
Connective Tissues
Connective tissues are made up of a matrix consisting of living cells anda
non-living substance, called the ground substance. The ground substance is
made of an organic substance (usually a protein) and an inorganic substance
(usually a mineral or water). The principal cell of connective tissues is the
fibroblast. This cell makes the fibers found in nearly all of the connective
tissues. Fibroblasts are motile, able to carry out mitosis, and can synthesize
whichever connective tissue is needed. Macrophages, lymphocytes, and,
occasionally, leukocytes can be found in some connective tissues. Other
cells that can be found in different connective tissues provide functions that
are important for those specific tissues. For example, osteocytes (found in
bone) and adipocytes (found in fat) are specialized cells that are critical for
the formation and function of those tissues.
The organic portion or protein fibers found in connective tissues are either
collagen, elastic, or reticular fibers. Collagen fibers provide strength to the
tissue, preventing it from being torn or separated from the surrounding
tissues. Elastic fibers are made of the protein elastin; this fiber can stretch to
one and one half of its length and return to its original size and shape.
Elastic fibers provide flexibility to the tissues. Reticular fibers are the third
type of protein fiber found in connective tissues. This fiber consists of thin
strands of collagen that form a network of fibers to support the tissue and
other organs to which it is connected. The various types of connective
tissues, the types of cells and fibers they are made of, and sample locations
of the tissues is summarized in [link].
Connective Tissues
Tissue Cells Fibers Location
fibroblasts,
macrophages, around blood
few: collagen,
some : vessels;
loose/areolar elastic,
lymphocytes, ; anchors
reticular ; .
some epithelia
neutrophils
Connective Tissues
Tissue Cells
dense,
fibrous fibroblasts,
connective macrophages,
tissue
chondrocytes,
cartilage chondroblasts
osteoblasts,
bone osteocytes,
osteoclasts
adipose adipocytes
red blood
blood cells, white
blood cells
Loose/Areolar Connective Tissue
Fibers
mostly
collagen
hyaline: few
collagen
fibrocartilage:
large amount
of collagen
some:
collagen,
elastic
few
none
Location
irregular:
skin regular:
tendons,
ligaments
shark
skeleton,
fetal bones,
human ears,
intervertebral
discs
vertebrate
skeletons
adipose (fat)
blood
Loose connective tissue, also called areolar connective tissue, has a
sampling of all of the components of a connective tissue. As illustrated in
[link], loose connective tissue has some fibroblasts; macrophages are
present as well. In this figure, collagen fibers are relatively wide and stain a
light pink, while elastic fibers are thin and stain dark blue to black. The
space between the formed elements of the tissue is filled with the matrix.
The material in the connective tissue gives it a loose consistency similar to
a cotton ball that has been pulled apart. Loose connective tissue is found
around every blood vessel and helps to keep the vessel in place. The tissue
is also found around and between most body organs. In summary, areolar
tissue is tough, yet flexible.
Elastin fiber Fibroblasts Collagen fiber
Loose connective tissue is
composed of loosely woven
collagen and elastic fibers. The
fibers and other components of the
connective tissue matrix are
secreted by fibroblasts.
Fibrous Connective Tissue
Fibrous connective tissues contain large amounts of collagen fibers and few
cells or matrix material. The fibers can be arranged irregularly or regularly
with the strands lined up in parallel. Irregularly arranged fibrous connective
tissues are found in areas of the body where stress occurs from all
directions, such as the dermis of the skin. Regular fibrous connective tissue,
shown in [link], is found in tendons (which connect muscles to bones) and
ligaments (which connect bones to bones).
Fibroblast nuclei Fibroblasts Collagen fibers
Fibrous connective tissue
from the tendon has strands
of collagen fibers lined up
in parallel.
Cartilage
Cartilage is a connective tissue with a large amount of extracellular matrix
and variable amounts of fibers. The cells, called chondrocytes, make the
matrix and fibers of the tissue. Chondrocytes are found in spaces within the
tissue (lacunae).
A cartilage with few collagen and elastic fibers is hyaline cartilage,
illustrated in [link]. The lacunae are randomly scattered throughout the
tissue and the matrix takes on a milky or scrubbed appearance with routine
histological stains. Sharks have cartilaginous skeletons, as does nearly the
entire human skeleton during a specific pre-birth developmental stage. A
remnant of this cartilage persists in the outer portion of the human nose.
Hyaline cartilage is also found at the ends of long bones, reducing friction
and cushioning the articulations of these bones.
Hyaline cartilage
consists of a matrix
with cells called
chondrocytes
embedded in it. The
chondrocytes exist in
cavities in the matrix
called lacunae.
Elastic cartilage has a large amount of elastic fibers, giving it tremendous
flexibility. The ears of most vertebrate animals contain this cartilage as do
portions of the larynx, or voice box. Fibrocartilage contains a large amount
of collagen fibers, giving the tissue tremendous strength. Fibrocartilage
comprises the intervertebral discs in vertebrate animals. Hyaline cartilage
found in movable joints such as the knee and shoulder becomes damaged as
a result of age or trauma. Damaged hyaline cartilage is replaced by
fibrocartilage and results in the joints becoming “stiff.”
Bone
Bone, or osseous tissue, is a connective tissue that has a large amount of
two different types of matrix material. The organic matrix is similar to the
matrix material found in other connective tissues, including some amount of
collagen and elastic fibers. This gives strength and flexibility to the tissue.
The inorganic matrix consists of mineral salts—mostly calcium phosphate
—that give the tissue hardness. In most organisms, bone is being remodeled
by the action of cells called osteoclasts and osteoblasts (see below).
There are three types of cells in bone: osteoblasts, osteocytes, and
osteoclasts. Osteoblasts are active in making bone for growth and
remodeling. Osteoblasts deposit bone material into the matrix and, after the
matrix surrounds them, they continue to live, but in a reduced metabolic
state as osteocytes. Osteocytes are found in lacunae of the bone. Osteoclasts
are active in breaking down bone for bone remodeling, and they provide
access to calcium stored in tissues. Osteoclasts are usually found on the
surface of the tissue.
Bone can be divided into two types: compact and spongy. Compact bone is
found in the shaft (or diaphysis) of a long bone and the surface of the flat
bones, while spongy bone is found in the end (or epiphysis) of a long bone.
Compact bone is organized into subunits called osteons, as illustrated in
[link]. A blood vessel and a nerve are found in the center of the structure
within the Haversian canal, with radiating circles of lacunae around it
known as lamellae. The wavy lines seen between the lacunae are
microchannels called canaliculi; they connect the lacunae to aid diffusion
between the cells. Spongy bone is made of tiny plates called trabeculae
these plates serve as struts to give the spongy bone strength. Over time,
these plates can break causing the bone to become less resilient.
Spongy bone
Compact “\s>
7 N
Lymphatic vessel
Nerve
Blood vessels
Trabeculae
Spongy bone
x Osteocyte
SOP IN —$— Lamellae
peers SS (concentric circles)
Pir Osteoclast
Haversian
canal
= Canaliculi
(canals radiating
outward)
Osteoblast
LSI AKG A KH ))
Or
ee
Canaliculae
Lamellae
(a) Compact bone is a dense matrix on the outer surface of
bone. Spongy bone, inside the compact bone, is porous with
web-like trabeculae. (b) Compact bone is organized into rings
called osteons. Blood vessels, nerves, and lymphatic vessels
are found in the central Haversian canal. Rings of lamellae
surround the Haversian canal. Between the lamellae are
cavities called lacunae. Canaliculi are microchannels
connecting the lacunae together. (c) Osteoblasts surround the
exterior of the bone. Osteoclasts bore tunnels into the bone and
osteocytes are found in the lacunae.
Adipose Tissue
Adipose tissue, or fat tissue, is considered a connective tissue even though
it does not have fibroblasts or a real matrix, and only has a few fibers.
Adipose tissue is made up of cells called adipocytes (descendants of
fibroblasts) that collect and store fat in the form of triglycerides. Adipose
tissues serve as energy stores, and additionally serve as insulation to help
maintain body temperatures, allowing animals to be endothermic. They also
function as cushions to prevent damage to body organs. Under a
microscope, adipose tissue cells appear empty due to the extraction of fat
during the processing of the material for viewing, as seen in [link]. The thin
lines in the image are the plasma membranes, and the nuclei are the small,
black dots at the edges of the cells.
Adipose is a connective tissue
is made up of cells called
adipocytes. Adipocytes have
small nuclei localized at the
cell edge. The interior of these
large cells is filled with
triglycerides, commonly known
as "fat".
Blood
Blood is considered a connective tissue because it has a fluid matrix
(plasma) and is derived from the germ layer known as mesoderm. . The
living cell types are red blood cells (RBC), also called erythrocytes, and
white blood cells (WBC), also called leukocytes ({link]).
Neutrophil
Macrophage BX & © © ©
— Monocyte
'
© Q Lymphocyte
a
® ...
Basophil
v9 "
\ de @
© %.
- niesd “@
ad
@.%
Platelets
Blood is a connective tissue that has a fluid matrix,
called plasma, and no fibers. Erythrocytes (red blood
cells), the predominant cell type, are involved in the
transport of oxygen and carbon dioxide. Also present
are various leukocytes (white blood cells) involved in
immune response.
The cell found in greatest abundance in blood is the erythrocyte, or red
blood cell ("erythro" = red). The principal function of an erythrocyte is to
carry and deliver oxygen to the tissues. There are millions of erythrocytes in
every milliliter of your blood. Mammalian erythrocytes lose their nuclei and
mitochondria when they mature and are released from the bone marrow
where they are generated. Fish, amphibian, and avian red blood cells
maintain their nuclei and mitochondria throughout the cell’s life.
Leukocytes, or white blood cells ("leuko" = white), are the other main
cellular component of blood. There are 5,000-10,000 leukocytes in every
milliliter of your blood. These include cells called lymphocytes, as well as
neutrophils, monocytes, and others. Lymphocytes function primarily in the
immune response to foreign antigens or material, which you will learn in
more detail later in this unit. Neutrophils are phagocytic (they engulf other
cells or objects and digest them) cells, and they participate in one of the
early lines of defense against microbial invaders or fungal invaders.
Another leukocyte that is found in the peripheral blood is the monocyte.
Monocytes give rise to phagocytic macrophages that clean up dead and
damaged cells in the body, whether they are foreign or from the host
animal. Two additional leukocytes in the blood are eosinophils and
basophils—both help to facilitate the inflammatory response.
The slightly granular material among the cells in [link] are cytoplasmic
fragments of cells formed in the bone marrow. These are called platelets or
thrombocytes. Platelets are a key player in the formation of blood clots,
which are important in keeping your blood in your body when you get cut
or scraped.
Muscle Tissues
There are three types of muscle in animal bodies: smooth, skeletal, and
cardiac. They differ by the presence or absence of striations or bands, the
number and location of nuclei, whether they are voluntarily or involuntarily
controlled, and their location within the body. [link] summarizes these
differences. You will learn more about these cells and their functions later
in this unit
Types of Muscles
Type
of
Muscle Striations Nuclei Control Location
smooth no eon involuntary visceral
many, at keletal
skeletal yes me voluntary en
periphery muscles
ingle, in ;
cardiac yes eee involuntary heart
center
Smooth Muscle
Smooth muscle does not have striations in its cells. It has a single, centrally
located nucleus, as shown in [link]. Constriction of smooth muscle occurs
under involuntary, autonomic nervous control and in response to local
conditions in the tissues. Smooth muscle tissue is also called non-striated as
it lacks the banded appearance of skeletal and cardiac muscle. The walls of
blood vessels, the tubes of the digestive system, and the tubes of the
reproductive systems are composed of mostly smooth muscle.
Smooth muscle cells Skeletal muscle cells Cardiac muscle cells
————— SS
—————— SS
; Intercalated disc
Smooth muscle cells do not have striations, while skeletal
muscle cells do. Cardiac muscle cells have striations, but,
unlike the multinucleate skeletal cells, they have only one
nucleus. Cardiac muscle tissue also has intercalated discs,
specialized regions running along the plasma membrane
that join adjacent cardiac muscle cells and assist in passing
an electrical impulse from cell to cell.
Skeletal Muscle
Skeletal muscle has striations across its cells caused by the arrangement of
the contractile proteins actin and myosin. These muscle cells are relatively
long and have multiple nuclei along the edge of the cell. Skeletal muscle is
under voluntary, somatic nervous system control and is found in the
muscles that move bones. [link] illustrates the histology of skeletal muscle.
Cardiac Muscle
Cardiac muscle, shown in [link], is found only in the heart. Like skeletal
muscle, it has cross striations in its cells, but cardiac muscle has a single,
centrally located nucleus. Cardiac muscle is not under voluntary control but
can be influenced by the autonomic nervous system to speed up or slow
down. A structure found only in cardiac muscle cells is is at the end of the
cell where it abuts the next cardiac cell in the row. This structure is called
an intercalated disc: it assists in passing electrical impulses efficiently from
one cell to the next, and maintains the strong synchrony needed to make the
heart chambers work together efficiently.
Nervous Tissues
Nervous tissues are made of cells specialized to receive and transmit
electrical impulses from specific areas of the body and to send them to
specific locations in the body. The main cell of the nervous system is the
neuron, illustrated in [link]. The large structure with a central nucleus is the
cell body of the neuron. Projections from the cell body are either dendrites
specialized in receiving input or a single axon specialized in transmitting
impulses. Some glial cells are also shown. Astrocytes regulate the chemical
environment of the nerve cell, and oligodendrocytes insulate the axon so the
electrical nerve impulse is transferred more efficiently. Other glial cells that
are not shown support the nutritional and waste requirements of the neuron.
Some of the glial cells are phagocytic and remove debris or damaged cells
from the tissue. A nerve in your body consists of neurons and glial cells.
Cell body (soma)
Axon Oligodendrocyte
Dendrites
Astrocyte
Axon terminals lt
The neuron has projections called
dendrites that receive signals and
projections called axons that send
signals. Also shown are two types
of glial cells: astrocytes regulate
the chemical environment of the
nerve cell, and oligodendrocytes
insulate the axon so the electrical
nerve impulse is transferred more
efficiently.
Sponges and Cnidarians
Introduction
"Jellyfish are 97% water or something, so how much are they doing? Just
give them another 3% and make them water. It's more useful." Karl
Pilkington, Handslapped by a Jellyfish, 2007
Jellyfish
Jellyfish in the Monterey Aquarium, Monterey
California. Image courtesy of David A. Rintoul
Pilkington's disdain for the jellyfish (a member of the group of animals we
call Cnidarians) is misplaced. Jellyfish, besides being spectacular and fun to
watch, also provide food for other marine animals, including sea turtles.
These simple animals have been around for a long time, and can also teach
us lots of lessons about animals and animal evolution.
The kingdom of animals is informally divided into invertebrate animals,
those without a backbone, and vertebrate animals, those with a backbone.
Although we are most familiar with vertebrate animals, the vast majority of
animal species, about 95 percent, are invertebrates. Invertebrates include
millions of species in about 32 phyla, and we will only hit the highlights in
the subsequent sections of this text.
The sponges and the cnidarians represent the simplest of animals. Sponges
appear to represent an early stage of multicellularity in the animal clade.
Although they have specialized cells for particular functions, they lack true
tissues in which specialized cells are organized into functional groups.
Sponges are similar to what might have been the ancestor of animals: a
colonial, flagellated protist. The cnidarians, or the jellyfish and their kin, are
the simplest animal group that displays true tissues, although they possess
only two tissue layers.
Sponges
Animals in subkingdom Parazoa represent the simplest animals and include
the sponges, or phylum Porifera ({link]). All sponges are aquatic and the
majority of species are marine. Sponges live in intimate contact with water,
which plays a role in their feeding, gas exchange, and excretion. Much of
the body structure of the sponge is dedicated to moving water through the
body so it can filter out food, absorb dissolved oxygen, and eliminate
wastes.
Sponges are members of the phylum Porifera,
which contains the simplest animals. (credit:
Andrew Turmer)
The body of the simplest sponges takes the shape of a cylinder with a large
central cavity, the spongocoel. Water enters the spongocoel from numerous
pores in the body wall. Water flows out through a large opening called the
osculum ([link]). However, sponges exhibit a diversity of body forms,
which vary in the size and branching of the spongocoel, the number of
osculi, and where the cells that filter food from the water are located.
Sponges consist of an outer layer of flattened cells and an inner layer of
cells called choanocytes separated by a jelly-like substance called mesohyl.
The mesohyl contains embedded amoeboid cells that secrete tiny needles
called spicules or protein fibers that help give the sponge its structural
strength. The cell body of the choanocyte is embedded in mesohy]l but
protruding into the spongocoel is a mesh-like collar surrounding a single
flagellum. The beating of flagella from all choanocytes moves water
through the sponge. Food particles are trapped in mucus produced by the
sieve-like collar of the choanocytes and are ingested by phagocytosis and
digested within those cells. Amoebocytes take up nutrients repackaged in
food vacuoles of the choanocytes and deliver them to other cells within the
sponge.
Osculum
Mesohyl
Basic sponge body plan
The sponge’s basic body plan is
shown.
Reproduction in Sponges
Despite their lack of complexity, sponges are clearly successful organisms,
having persisted on Earth for more than half a billion years. Lacking a true
digestive system, sponges depend on the intracellular digestive processes of
their choanocytes for their energy intake. The limit of this type of digestion
is that food particles must be smaller than individual cells. Gas exchange,
circulation, and excretion occur by diffusion between cells and the water.
Sponges reproduce both sexually and asexually. Asexual reproduction is
either by fragmentation (in which a piece of the sponge breaks off and
develops into a new individual), or budding (an outgrowth from the parent
that eventually detaches). But sponges are also capable of producing
gametes, although both types of gametes can be produced in the same
individual (hermaphroditism). Sponges may be sequentially
hermaphroditic, producing eggs first and sperm later. Eggs arise from
amoebocytes and are retained within the spongocoel, whereas sperm arise
from choanocytes are ejected via the osculum. These sperm are carried by
the water and fertilize the eggs of other sponges. Larval development starts
with the sponge, and free-swimming larvae are then released via the
osculum. This is the only time that sponges exhibit one of the hallmarks of
the animal kingdom, motility. The larvae then attach to a substrate and
spend their adult lives in the same spot.
Cnidarians
The phylum Cnidaria includes animals that show radial symmetry and are
diploblastic (have two germ layers instead of the three). Nearly all (about
99 percent) cnidarians are marine species, but there are freshwater jellyfish,
even in Kansas! Cnidarians have specialized cells known as cnidocytes
(“stinging cells”) containing organelles called nematocysts. These cells are
concentrated around the mouth and tentacles of the animal and can
immobilize prey with toxins. Nematocysts contain coiled threads that may
bear barbs. The outer wall of the cell has a hairlike projection that is
sensitive to touch. When touched, the cells fire the toxin-containing coiled
threads that can penetrate and stun the predator or prey (see [link]).
Touch-sensitive
hairlike projection
Cnidocyte X(
Thread
(a) Nematocyst with stored (b) Nematocyst after
thread and barb firing
Animals from the phylum Cnidaria have
stinging cells called cnidocytes. Cnidocytes
contain large organelles called (a) nematocysts
that store a coiled thread and barb. When
hairlike projections on the cell surface are
touched, (b) the thread, barb, and a toxin are
fired from the organelle.
Cnidarians display two distinct body plans: polyp or “stalk” and medusa or
“bell” ({link]). Examples of the polyp form are freshwater species of the
genus Hydra; perhaps the best-known medusoid animals are the jellies
(jellyfish). Polyps are sessile as adults, with a single opening to the
digestive system (the mouth) facing up with tentacles surrounding it.
Medusae are motile, with the mouth and tentacles hanging from the bell-
shaped body. In other cnidarians, both a polyp and medusa form exist, and
the life cycle alternates between these forms.
Mesoglea
(a) Medusa (b) Polyp
Cnidarians have two distinct body plans,
the (a) medusa and the (b) polyp. All
cnidarians have two tissue layers, with a
jelly-like mesoglea between them.
Physiological Processes of Cnidarians
All cnidarians have two tissue layers. The outer layer is called the
epidermis, whereas the inner layer is called the gastrodermis and lines the
digestive cavity. Between these two layers is a non-living, jelly-like
mesoglea. There are differentiated cell types in each tissue layer, such as
nerve cells, enzyme-secreting cells, and nutrient-absorbing cells, as well as
intercellular connections between the cells. However, organs and organ
systems are not present in this phylum.
The nervous system is primitive, with nerve cells scattered across the body
in a network. The function of the nerve cells is to carry signals from sensory
cells and to contractile cells. Groups of cells in the nerve net form nerve
cords that may be essential for more rapid transmission. Cnidarians perform
extracellular digestion, with digestion completed by intracellular digestive
processes. Food is taken into the gastrovascular cavity, enzymes are
secreted into the cavity, and the cells lining the cavity absorb the nutrient
products of the extracellular digestive process. The gastrovascular cavity
has only one opening that serves as both a mouth and an anus (an
incomplete digestive system). Like the sponges, Cnidarian cells exchange
oxygen, carbon dioxide, and nitrogenous wastes by diffusion between cells
in the epidermis and gastrodermis with water.
Flatworms, Nematodes, and Arthropods
Introduction
"“Tn the last ten years we have come to realize humans are more like worms
than we ever imagined.”" Bruce Alberts, American scientist and editor of
Science magazine
The use of a simple nematode, Caenorhabditis elegans, as a model system
for developmental biology has indeed revealed many similarities between
that simple creature and ourselves. The animal phyla of this and subsequent
modules are triploblastic (i.e., have THREE primary germ layers,
ectoderm, endoderm and mesoderm in the embryo). They have an
embryonic mesoderm sandwiched between the ectoderm and endoderm.
Most of these phyla are also bilaterally symmetrical, meaning that a
longitudinal section will divide them into right and left sides that are mirror
images of each other. Associated with bilateralism is the beginning of
cephalization, the evolution of a concentration of nervous tissues and
sensory organs in the head of the organism, which is where the organism
first encounters its environment.
The flatworms are acoelomate organisms that include free-living and
parasitic forms. The nematodes, or roundworms, possess a pseudocoelom
and consist of both free-living and parasitic forms. Finally, the arthropods,
one of the most successful taxonomic groups on the planet, are coelomate
organisms with a hard exoskeleton and jointed appendages.
Flatworms
Physiological Processes of Flatworms
Most flatworms are parasitic, including important parasites of humans.
Free-living species of flatworms are predators or scavengers, whereas
parasitic forms feed from the tissues of their hosts. Digestion is
extracellular, with enzymes secreted into the gut interior by cells lining the
tract, and digested materials taken into the same cells by phagocytosis. One
group, the cestodes, does not have a digestive system, because their
parasitic lifestyle and the environment in which they live (suspended within
the digestive cavity of their host) allows them to absorb nutrients directly
across their body wall. Flatworms have an excretory system with a network
of tubules throughout the body that open to the environment and nearby
flame cells, whose cilia beat to direct waste fluids concentrated in the
tubules out of the body. The system is responsible for regulation of
dissolved salts and excretion of nitrogenous wastes. The nervous system
consists of a pair of nerve cords running the length of the body with
connections between them and a large ganglion or concentration of nerve
cells at the anterior end of the worm; here, there may also be a
concentration of photosensory and chemosensory cells ({Link]).
Transverse
nerve Intestine Pharynx
Eyespot
Cerebral ganglia
Longitudinal nerve cords
Peripheral nerves
Nucleus
Excretory canal
Flame cell
This planarian is a free-living flatworm that has an
incomplete digestive system, an excretory system with a
network of tubules throughout the body, and a nervous
system made up of nerve cords running the length of the
body with a concentration of nerves and photosensory
and chemosensory cells at the anterior end.
Since there is no circulatory or respiratory system, gas and nutrient
exchange is dependent on diffusion and intercellular junctions. This
necessarily limits the thickness of the body in these organisms, constraining
them to be “flat” worms. Most flatworm species are monoecious
(hermaphroditic, possessing both sets of sex organs), and fertilization is
typically internal. Asexual reproduction is common in some groups in
which an entire organism can be regenerated from just a part of itself.
Nematodes
The phylum Nematoda, or roundworms, includes more than 28,000 species
with an estimated 16,000 parasitic species. The name Nematoda is derived
from the Greek word “nemos,” which means “thread.” Nematodes are
present in all habitats and are extremely common, although they are usually
not visible ({link]).
Head ganglion Cuticle Dorsalnerve Testis
Mouth Pharynx Intestine — Ventral nerve Anus
(b)
(a) An scanning electron micrograph of
the nematode Heterodera glycines and
(b) a schematic representation of the
anatomy of a nematode are shown.
(credit a: modification of work by
USDA, ARS; scale-bar data from Matt
Russell)
Most nematodes look similar to each other: slender tubes, tapered at each
end ([{link]). Nematodes are pseudocoelomates and have a complete
digestive system with a distinct mouth and anus.
The nematode body is encased in a cuticle, a flexible but tough exoskeleton,
or external skeleton, which offers protection and support. The cuticle
contains a carbohydrate-protein polymer called chitin. The cuticle also lines
the pharynx and rectum. Although the exoskeleton provides protection, it
restricts growth, and therefore must be continually shed and replaced as the
animal increases in size.
A nematode’s mouth opens at the anterior end with three or six lips and, in
some species, teeth in the form of cuticular extensions. There may also be a
sharp stylet that can protrude from the mouth to stab prey or pierce plant or
animal cells. The mouth leads to a muscular pharynx and intestine, leading
to the rectum and anal opening at the posterior end.
Physiological Processes of Nematodes
In nematodes, the excretory system is not specialized. Nitrogenous wastes
are removed by diffusion. In marine nematodes, regulation of water and salt
is achieved by specialized glands that remove unwanted ions while
maintaining internal body fluid concentrations.
Most nematodes have four nerve cords that run along the length of the body
on the top, bottom, and sides. The nerve cords fuse in a ring around the
pharynx, to form a head ganglion or “brain” of the worm, as well as at the
posterior end to form the tail ganglion. Beneath the epidermis lies a layer of
longitudinal muscles that permits only side-to-side, wave-like undulation of
the body.
Nematodes employ a diversity of sexual reproductive strategies depending
on the species; they may be monoecious, dioecious (Separate sexes), or may
reproduce asexually by parthenogenesis. Caenorhabditis elegans is nearly
unique among animals in having both self-fertilizing hermaphrodites and a
male sex that can mate with the hermaphrodite.
Arthropoda
The name of this phylum, “Arthropoda” means “jointed legs,” which aptly
describes each of the enormous number of species belonging to this
phylum. An estimated 85 percent of known species belong to this phylum,
with many more still undiscovered or undescribed. Insects form the largest
single group within the phylum. The principal characteristics of all the
animals in this phylum are functional segmentation of the body and the
presence of jointed appendages ([link]). Arthropods also have an
exoskeleton made principally of chitin. Arthropods are true coelomate
animals and exhibit protostomic development.
Trilobites, like the one in this fossil, are
an extinct group of arthropods. (credit:
Kevin Walsh)
Physiological Processes of Arthropods
A unique feature of arthropods is the presence of a segmented body with
fusion of certain sets of segments to give rise to functional segments. Fused
segments may form a head, thorax, and abdomen, or a cephalothorax and
abdomen, or a head and trunk. The coelom takes the form of a hemocoel (or
blood cavity). The open circulatory system, in which blood bathes the
internal organs rather than circulating in vessels, is powered by a two-
chambered heart. Respiratory systems vary, depending on the group of
arthropod: Insects and myriapods use a series of tubes (tracheae) that
branch throughout the body, open to the outside through openings called
spiracles, and perform gas exchange directly between the cells and air in the
tracheae. Aquatic crustaceans use gills, arachnids employ “book lungs,” and
aquatic chelicerates use “book gills.” The book lungs of arachnids are
internal stacks of alternating air pockets and hemocoel tissue shaped like
the pages of a book. The book gills of crustaceans are external structures
similar to book lungs with stacks of leaf-like structures that exchange gases
with the surrounding water ([link]).
Book gills
Cephalothorax
Book lung
(a) (b)
The book lungs of (a) arachnids are made up of
alternating air pockets and hemocoel tissue shaped like a
stack of books. The book gills of (b) crustaceans are
similar to book lungs but are external so that gas
exchange can occur with the surrounding water. (credit a:
modification of work by Ryan Wilson based on original
work by John Henry Comstock; credit b: modification of
work by Angel Schatz)
Arthropod Diversity
Phylum Arthropoda includes animals that have been successful in
colonizing terrestrial, aquatic, and aerial habitats. The phylum is further
classified into five subphyla: Trilobitomorpha (trilobites), Hexapoda
(insects and relatives), Myriapoda (millipedes, centipedes, and relatives),
Crustacea (crabs, lobsters, crayfish, isopods, barnacles, and some
zooplankton), and Chelicerata (horseshoe crabs, arachnids, scorpions, and
daddy longlegs). Trilobites are an extinct group of arthropods found from
the Cambrian period (540—490 million years ago) until they became extinct
in the Permian (300-251 million years ago) that are probably most closely
related to the Chelicerata. The 17,000 described species have been
identified from fossils ([link]).
Abdomen Thorax
Head
Dorsal blood
vessel Cerebral
AN) ganglion
Anus
Intestine
Spiracles
The basic anatomy of a representative
arthropod, in this case an insect, or
hexapod. Note that insects have a
developed digestive system (yellow), a
respiratory system (blue), a circulatory
system (red), and a nervous system
(purple).
Mollusks and Annelids
Introduction
"Clams are very conservative. They voted against having heads in the
Ordovician Period and have stuck to it ever since." Will Cuppy, American
humorist, in How to Attract the Wombat, 1949
The mollusks are a diverse group (85,000 described species) of mostly
marine species. They have a variety of forms, ranging from large predatory
squid and octopus, some of which show a high degree of intelligence, to
small grazing forms with elaborately sculpted and colored shells. The
annelids traditionally include the oligochaetes, which include the
earthworms and leeches, the polychaetes, which are a marine group, and
two other smaller classes.
Phylum Mollusca
An Edible Mollusk
Some mollusks are edible, like these Black Abalone (Haliotis
cracherodii), cruising in a tide pool of the coast of California. This
gastropod mollusk shows several of the features of many members of
this phylum, including a sturdy shell and a muscular foot. However,
due to overharvesting of this species, its populations are declining
and it can no longer be legally taken. "Abalone OCA" by Little
Mountain 5 - Own work. Licensed under Creative Commons
Attribution-Share Alike 3.0 via Wikimedia Commons.
Mollusca is the predominant phylum in marine environments; it is
estimated that 23 percent of all known marine species belong to this
phylum. It is the second most diverse phylum of animals with over 75,000
described species. The name “mollusca” signifies a soft body, as the earliest
descriptions of mollusks came from observations of unshelled, soft-bodied
cuttlefish (squid relatives). Although mollusk body forms vary, they share
key characteristics, such as a ventral, muscular foot that is typically used for
locomotion; the visceral mass, which contains most of the internal organs of
the animal; and a dorsal mantle, which is a flap of tissue over the visceral
mass that creates a space called the mantle cavity. The mantle may or may
not secrete a shell of calcium carbonate. In addition, many mollusks have a
scraping structure at the mouth, called a radula ([Link]).
The muscular foot varies in shape and function, depending on the type of
mollusk. It is a retractable as well as extendable organ, used for locomotion
and anchorage. Mollusks are eucoelomates, but the coelomic cavity is
restricted to a cavity around the heart in adult animals. The mantle cavity,
formed inside the mantle, develops independently of the coelomic cavity. It
is a multi-purpose space, housing the gills, the anus, organs for sensing food
particles in the water, and an outlet for gametes. Most mollusks have an
open circulatory system with a heart that circulates the hemolymph in open
Spaces around the organs. The octopuses and squid are an exception to this
and have a closed circulatory system with two hearts that move blood
through the gills and a third, systemic heart that pumps blood through the
rest of the body.
Mantle Coelom Intestine Gonad Shell
Anus
Digestive
gland
Stomach
Foot
Mouth
Nerve Visceral
Radula cords Crop mass Heart
There are many species and variations of
mollusks; the gastropod mollusk anatomy
is shown here, which shares many
characteristics common with other
groups.
Annelida
Phylum Annelida are segmented worms found in marine, terrestrial, and
freshwater habitats, but the presence of water or humidity is a critical factor
for their survival in terrestrial habitats. The name of the phylum is derived
from the Latin word annellus, which means a small ring. Approximately
16,500 species have been described. The phylum includes earthworms,
polychaete worms, and leeches. Like mollusks, annelids exhibit protostomic
development.
Annelids are bilaterally symmetrical and have a worm-like appearance.
Their particular segmented body plan results in repetition of internal and
external features in each body segment. This type of body plan is called
metamerism. The evolutionary benefit of such a body plan is thought to be
the capacity it allows for the evolution of independent modifications in
different segments that perform different functions. The overall body can
then be divided into head, body, and tail.
Physiological Processes of Annelida
The skin of annelids is protected by a cuticle that is thinner than the cuticle
of nematodes and arthropods, and it does not need to be molted for growth.
Chitinous hairlike extensions, anchored in the skin and projecting from the
cuticle, called chaetae, are present in every segment in most groups. The
chaetae are a defining character of annelids. Beneath the cuticle there are
two layers of muscle, one running around its circumference (circular) and
one running the length of the worm (longitudinal). Annelids have a true
coelom in which organs are distributed and bathed in coelomic fluid.
Annelids possess a well-developed complete digestive system with
specialized organs: mouth, muscular pharynx, esophagus, and crop. A
cross-sectional view of a body segment of an earthworm is shown in [link];
each segment is limited by a membrane that divides the body cavity into
compartments.
Annelids have a closed circulatory system with muscular pumping “hearts”
in the anterior segments, dorsal and ventral blood vessels that run the length
of the body with connections in each segment, and capillaries that service
individual tissues. Gas exchange occurs across the moist body surface.
Excretion is carried out by pairs of primitive “kidneys” called
metanephridia that consist of a convoluted tubule and an open, ciliated
funnel present in every segment. Annelids have a well-developed nervous
system with two ventral nerve cords and a nerve ring of fused ganglia
present around the pharynx.
Dorsal blood vessel
Chaetae
Nephridium
Intestine Ventral blood vessel
Ventral nerve cord
In this schematic showing the basic
anatomy of annelids, the digestive system
is indicated in green, the nervous system
is indicated in yellow, and the circulatory
system is indicated in red.
Annelids may be either monoecious (hermaphroditic, capable of producing
both male and female gametes), such as earthworms and leeches) or
dioecious (indivduals are either male or female), as is the case for
polychaetes.
Echinoderms and Chordates
Introduction
"Here’s a little lesson in deuterostome taxonomy for everyone out there.
These are animals in which the first embryonic opening become the anus,
and the second opening becomes the mouth (the name literally means
mouth second). This is in contrast the majority of animals, which form their
mouth first." RPM, author of the Evolgen blog, 2008
The phyla Echinodermata and Chordata (which includes the vertebrates)
and two smaller phyla are the members of the Deuterstomes. Deuterostomes
share similar patterns of early development, as noted above, which
distinguish them from most of the other animals.
Echinoderms
Echinodermata are named for their spiny skin (from the Greek “echinos”
meaning “spiny” and “dermos” meaning “skin”). The phylum includes
about 7,000!22D9te] described living species, such as sea stars, sea
cucumbers, sea urchins, sand dollars, and brittle stars. Echinodermata are
exclusively marine.
“Number of Living Species in Australia and the World,” A.D. Chapman,
Australia Biodiversity Information Services, last modified August 26, 2010,
http://www.environment.gov.au/biodiversity/abrs/publications/other/species
-numbers/2009/03-exec-summary.html.
Although the early larval stages of all echinoderms have bilateral symmetry,
adult echinoderms exhibit pentaradial symmetry and have an endoskeleton
made of ossicles ([{link]). The endoskeleton is developed by epidermal cells,
which may also possess pigment cells, giving vivid colors to these animals,
as well as cells laden with toxins. These animals have a true coelom, a
portion of which is modified into a unique circulatory system called a water
vascular system. An interesting feature of these animals is their power to
regenerate, even when over 75 percent of their body mass is lost.
Physiological Processes of Echinoderms
Echinoderms have a unique system for gas exchange, nutrient circulation,
and locomotion called the water vascular system. The system consists of a
central ring canal and radial canals extending along each arm. Water
circulates through these structures allowing for gas, nutrient, and waste
exchange. A structure on top of the body, called the madreporite, regulates
the amount of water in the water vascular system. “Tube feet,” which
protrude through openings in the endoskeleton, may be expanded or
contracted using the hydrostatic pressure in the system. The system allows
for slow movement, but a great deal of power, as witnessed when the tube
feet latch on to opposite halves of a bivalve mollusk, like a clam, and
slowly, but surely pull the shells apart, exposing the flesh within.
Madreporite
Central ring canal
Digestive glands
This diagram shows the anatomy of a sea Star.
The echinoderm nervous system has a nerve ring at the center and five
radial nerves extending outward along the arms. There is no centralized
nervous control. Echinoderms have separate sexes and release their gametes
into the water where fertilization takes place. Echinoderms may also
reproduce asexually through regeneration from body parts.
Echinoderm Diversity
This phylum is divided into five classes: Asteroidea (sea stars), Ophiuroidea
(brittle stars), Echinoidea (sea urchins and sand dollars), Crinoidea (sea
lilies or feather stars), and Holothuroidea (sea cucumbers) ([link]).
(d)
Different members of Echinodermata include the (a) sea
star in class Asteroidea, (b) the brittle star in class
Ophiuroidea, (c) the sea urchins of class Echinoidea, (d)
the sea lilies belonging to class Crinoidea, and (d) sea
cucumbers representing class Holothuroidea. (credit a:
modification of work by Adrian Pingstone; credit b:
modification of work by Joshua Ganderson; credit c:
modification of work by Samuel Chow; credit d:
modification of work by Sarah Depper; credit e:
modification of work by Ed Bierman)
Chordates
The majority of species in the phylum Chordata are found in the subphylum
Vertebrata, which include many species with which we are familiar. The
vertebrates contain more than 60,000 described species, divided into major
groupings of the lampreys, fishes, amphibians, reptiles, birds, and
mammals.
Animals in the phylum Chordata share four key features that appear at
some stage of their development: a notochord, a dorsal hollow nerve cord,
pharyngeal slits, and a post-anal tail ({link]). In certain groups, some of
these traits are present only during embryonic development.
The chordates are named for the notochord, which is a flexible, rod-shaped
structure that is found in the embryonic stage of all chordates and in the
adult stage of some chordate species. It is located between the digestive
tube and the nerve cord, and provides skeletal support through the length of
the body. In some chordates, the notochord acts as the primary axial support
of the body throughout the animal’s lifetime. In vertebrates, the notochord
is present during embryonic development, at which time it induces the
development of the neural tube and serves as a support for the developing
embryonic body. The notochord, however, is not found in the postnatal
stage of vertebrates; at this point, it has been replaced by the vertebral
column (the spine).
The dorsal hollow nerve cord is derived from ectoderm that sinks below
the surface of the skin and rolls into a hollow tube during development. In
chordates, it is located dorsally to the notochord. In contrast, other animal
phyla possess solid nerve cords that are located either ventrally or laterally.
The nerve cord found in most chordate embryos develops into the brain and
spinal cord, which compose the central nervous system.
Pharyngeal slits are openings in the pharynx, the region just posterior to
the mouth, that extend to the outside environment. In organisms that live in
aquatic environments, pharyngeal slits allow for the exit of water that enters
the mouth during feeding. Some invertebrate chordates use the pharyngeal
slits to filter food from the water that enters the mouth. In fishes, the
pharyngeal slits are modified into gill supports, and in jawed fishes, jaw
supports. In tetrapods, the slits are further modified into components of the
ear and tonsils, since there is no longer any need for gill supports in these
air-breathing animals. Tetrapod means “four-footed,” and this group
includes amphibians, reptiles, birds, and mammals. (Birds are considered
tetrapods because they evolved from tetrapod ancestors.)
The post-anal tail is a posterior elongation of the body extending beyond
the anus. The tail contains skeletal elements and muscles, which provide a
source of locomotion in aquatic species, such as fishes. In some terrestrial
vertebrates, the tail may also function in balance, locomotion, courting, and
signaling when danger is near. In many species, the tail is absent or
reduced; for example, in apes, including humans, it is present in the
embryo, but reduced in size and nonfunctional in adults.
Dorsal hollow
nerve cord
Notochord Post-anal tail
Pharyngeal slits
In chordates, four common features
appear at some point in development: a
notochord, a dorsal hollow nerve cord,
pharyngeal slits, and a post-anal tail. The
anatomy of a cephalochordate shown here
illustrates all of these features.
Invertebrate Chordates
In addition to the vertebrates, the phylum Chordata contains two clades of
invertebrates: Urochordata (tunicates) and Cephalochordata (lancelets).
Members of these groups possess the four distinctive features of chordates
at some point during their development.
The tunicates ([link]) are also called sea squirts. The name tunicate derives
from the cellulose-like carbohydrate material, called the tunic, which covers
the outer body. Although tunicates are classified as chordates, the adult
forms are much modified in body plan and do not have a notochord, a
dorsal hollow nerve cord, or a post-anal tail, although they do have
pharyngeal slits. The larval form possesses all four structures. Most
tunicates are hermaphrodites. Tunicate larvae hatch from eggs inside the
adult tunicate’s body. After hatching, a tunicate larva swims for a few days
until it finds a suitable surface on which it can attach, usually in a dark or
shaded location. It then attaches by the head to the substrate and undergoes
metamorphosis into the adult form, at which point the notochord, nerve
cord, and tail disappear.
Mouth Anus Dorsal hollow
nerve cord Pharyngeal
slits
Tunic
Anus
Heart
Pharyngeal Stomach Notocord
slits
Stomach Gonad
(a) (b) (c)
(a) This photograph shows a colony of the tunicate Botrylloides
violaceus. In the (b) larval stage, the tunicate can swim freely until it
attaches to a substrate to become (c) an adult. (credit a: modification
of work by Dr. Dwayne Meadows, NOAA/NMFS/OPR)
Lancelets possess a notochord, dorsal hollow nerve cord, pharyngeal slits,
and a post-anal tail in the adult stage ([link]). The notochord extends into
the head, which gives the subphylum its name (Cephalochordata). Extinct
fossils of this subphylum date to the middle of the Cambrian period (540—
488 mya).The living forms, the lancelets, are named for their blade-like
shape. Lancelets are only a few centimeters long and are usually found
buried in sand at the bottom of warm temperate and tropical seas. Like
tunicates, they are suspension feeders.
Adult lancelets retain the four key
features of chordates: a notochord, a
dorsal hollow nerve cord, pharyngeal
slits, and a post-anal tail.
Vertebrates
Introduction
"The development of the Vertebrate proceeds from an axis upward, in two
layers, which coalesce at the edges, and also downward, in two layers,
which likewise coalesce at the edges. Thus two main tubes are formed, one
above the other. During the formation of these, the embryo separates into
strata, so that the two main tubes are composed of subordinate tubes which
enclose each other as fundamental organs, and are capable of developing
into all the organs." Karl Ernst von Baer, German embryologist, 1828
Vertebrates are the largest and probably the most recognizable organisms of
the animal kingdom ([link]). More than 62,000 vertebrate species have been
identified. The vertebrate species now living represent only a small portion
of the vertebrates that have existed. The best-known extinct vertebrates are
the dinosaurs, a unique group of reptiles, reaching sizes not seen before or
since in terrestrial animals.
(a) (b) (c)
Examples of critically endangered vertebrate species include
(a) the Siberian tiger (Panthera tigris altaica), (b) the
Panamanian golden frog (Atelopus zeteki), and (c) the
Philippine eagle (Pithecophaga jefferyi). (credit a: modification
of work by Dave Pape; credit b: modification of work by Brian
Gratwicke; credit c: modification of work by
"cuatrok77"/Flickr)
Fishes
Modern fishes include an estimated 31,000 species. Fishes were the earliest
vertebrates, and jawless fishes were the earliest of these. Jawless fishes—
the present day hagfishes and lampreys—have a distinct cranium and
complex sense organs including eyes, distinguishing them from the
invertebrate chordates. The jawed fishes evolved later and are
extraordinarily diverse today. These include the cartilaginous fishes (e.g.
rays and sharks), with a skeleton made of cartilage, and the bony fishes,
which have a bony skeleton. All fishes are active feeders, rather than
sessile, suspension feeders.
Jawless fishes
Jawless fishes
ey
ae = :
(a) Jawless fishes include 67 species of hagfishes. These
Pacific hagfishes are scavengers that live on the ocean floor.
(b) Lampreys are another type of jawless fish. These parasitic
sea lampreys attach to their lake trout host by suction and use
their rough tongues to rasp away flesh in order to feed on the
trout’s blood. (credit a: modification of work by Linda Snook,
NOAA/CBNMS; credit b: modification of work by USGS)
Jawed fishes
Cartilaginous fishes
(a)
The jawed fishes include the clade Chondrichthyes, fishes with
skeletons made of cartilage, and these include the sharks and
rays(a) This hammerhead shark is an example of a predatory
cartilaginous fish. (b) This stingray blends into the sandy
bottom of the ocean floor when it is feeding or awaiting prey.
(credit a: modification of work by Masashi Sugawara; credit b:
modification of work by "Sailn1"/Flickr)
Sharks reproduce sexually and eggs are fertilized internally. Most species
are ovoviviparous, that is, the fertilized egg is retained in the oviduct of the
mother’s body, and the embryo is nourished by the egg yolk. The eggs
hatch in the uterus and young are born alive and fully functional. Some
species of sharks are oviparous: They lay eggs that hatch outside of the
mother’s body. Embryos are protected by a shark egg case or “mermaid’s
purse” that has the consistency of leather. The shark egg case has tentacles
that snag in seaweed and give the newborn shark cover. A few species of
sharks are viviparous, that is, the young develop within the mother’s body,
and she gives live birth.
Rays and skates include more than 500 species and are closely related to
sharks. They can be distinguished from sharks by their flattened bodies,
pectoral fins that are enlarged and fused to the head, and gill slits on their
ventral surface ({link]b). Like sharks, rays and skates have a cartilaginous
skeleton. Most species are marine and live on the sea floor, with nearly a
worldwide distribution.
Bony Fishes
Members of the clade Osteichthyes, or bony fishes, are characterized by a
bony skeleton. The vast majority of present-day fishes belong to this group,
which consists of approximately 30,000 species, making it the largest class
of vertebrates in existence today.
(a) (b)
The (a) sockeye salmon and (b) coelacanth are both bony
fishes of the Osteichthyes clade. The coelacanth,
sometimes called a lobe-finned fish, was thought to have
gone extinct in the Late Cretaceous period 100 million
years ago until one was discovered in 1938 between
Africa and Madagascar. (credit a: modification of work
by Timothy Knepp, USFWS; credit b: modification of
work by Robbie Cada)
Amphibians
Amphibians are vertebrate tetrapods. Amphibia includes the familiar frogs,
toads, and salamanders, as well as the caecilians, limbless amphibians that
superficially resemble worms and snakes. The term amphibian means “dual
life,” which is a reference to the metamorphosis that many frogs undergo
from a tadpole to an adult and the mixture of aquatic and terrestrial
environments in their life cycle. Amphibians evolved in the Devonian
period and were the earliest terrestrial tetrapods.
Amphibian Diversity
Amphibia comprise an estimated 6,500 extant species that inhabit tropical
and temperate regions around the world. Amphibians can be divided into
three clades: Urodela (“tailed-ones”’), the salamanders and newts; Anura
(“tail-less ones”), the frogs and toads; and Apoda (“legless ones”), the
caecilians.
Frogs and Salamanders
(a) (b)
There are about 500 species of salamanders and 5,000
species of frogs worldwide. (a) Salamanders are
terrestrial animals, but most are commonly found only
near water. (b) The Australian green tree frog is a
nocturnal predator that lives in the canopies of trees near
a water source. (credit a: modification of work by
Valentina Storti; credit b: modification of work by Evan
Pickett)
Caecilians comprise an estimated 185 species. They lack external limbs and
resemble giant earthworms. They inhabit soil and are found primarily in the
tropics of South America, Africa, and southern Asia where they are adapted
for a soil-burrowing lifestyle and are nearly blind. Unlike most of the other
amphibians that breed in or near water, reproduction in a drier soil habitat
means that caecilians must utilize internal fertilization, and most species
give birth to live young ((link]).
Caecilians lack external limbs and are
well adapted for a soil-burrowing
lifestyle. (credit: modification of work by
"cliff1066"/Flickr)
Reptiles and Birds
The amniotes—reptiles, birds, and mammals—are distinguished from
amphibians by their terrestrially adapted (shelled) egg and an embryo
protected by amniotic membranes. The evolution of amniotic membranes
meant that the embryos of amniotes could develop within an aquatic
environment inside the egg. This led to less dependence on a water
environment for development and allowed the amniotes to invade drier
areas. This was a significant evolutionary change that distinguished them
from amphibians, which were restricted to moist environments due to their
shell-less eggs. Although the shells of various amniotic species vary
significantly, they all allow retention of water. The membranes of the
amniotic egg also allowed gas exchange and sequestering of wastes within
the enclosure of an eggshell. The shells of bird eggs are composed of
calcium carbonate and are hard and brittle, but possess pores for gas and
water exchange. The shells of reptile eggs are more leathery and pliable.
Most mammals do not lay eggs; however, even with internal gestation,
amniotic membranes are still present.
In the past, the most common division of amniotes has been into classes
Mammalia, Reptilia, and Aves. Birds are descended, however, from
dinosaurs, so this classical scheme results in groups that are not true clades.
We will discuss birds as a group distinct from reptiles with the
understanding that this does not reflect evolutionary history.
Reptiles
Reptiles are tetrapods. Limbless reptiles—snakes—may have vestigial
limbs and, like caecilians, are classified as tetrapods because they are
descended from four-limbed ancestors. Reptiles lay shelled eggs on land.
Even aquatic reptiles, like sea turtles, return to the land to lay eggs. They
usually reproduce sexually with internal fertilization. Some species display
Ovoviviparity, with the eggs remaining in the mother’s body until they are
ready to hatch. Other species are viviparous, with the offspring born alive.
One of the key adaptations that permitted reptiles to live on land was the
development of their scaly skin, containing the protein keratin and waxy
lipids, which prevented water loss from the skin. This occlusive skin means
that reptiles cannot use their skin for respiration, like amphibians, and thus
all must breathe with lungs. In addition, reptiles conserve valuable body
water by excreting nitrogen in the form of uric acid paste. These
characteristics, along with the shelled, amniotic egg, were the major reasons
why reptiles became so successful in colonizing a variety of terrestrial
habitats far from water.
Reptiles are ectotherms, that is, animals whose main source of body heat
comes from the environment. Behavioral maneuvers, like basking to heat
themselves, or seeking shade or burrows to cool off, help them regulate
their body temperature,
Class Reptilia includes diverse species classified into four living clades.
These are the Crocodilia, Sphenodontia, Squamata, and Testudines.
The Crocodilia (“small lizard”) arose approximately 84 million years ago,
and living species include alligators, crocodiles, and caimans. Crocodilians
({link]a) live throughout the tropics of Africa, South America, the
southeastern United States, Asia, and Australia. They are found in
freshwater habitats, such as rivers and lakes, and spend most of their time in
water. Some species are able to move on land due to their semi-erect
posture.
4f Abs yd
(a) Crocodilians, such as this Siamese crocodile, provide
parental care for their offspring. (b) This Tuatara
(Sphenodon punctatus is one of only two species in the
Sphenodontia, and is found only in New Zealand. (c)
The garter snake belongs to the genus Thamnophis, the
most widely distributed reptile genus in North America.
(d) The African spurred tortoise lives at the southern
edge of the Sahara Desert. It is the third largest tortoise
in the world. (credit a: modification of work by Keshav
Mukund Kandhadai; credit b: courtesy of David A.
Rintoul; credit c: modification of work by Steve
Jurvetson; credit d: modification of work by Jim Bowen)
The Sphenodontia (“wedge tooth”) arose in the Mesozoic Era and includes
only one living genus, the Tuatara, with two species that are found in New
Zealand ([{link]b). There are many fossil species extending back to the
Triassic period (250-200 million years ago). Although the tuataras resemble
lizards, they are anatomically distinct and share characteristics that are
found in birds and turtles.
Squamata (“scaly”) arose in the late Permian; living species include lizards
and snakes, which are the largest extant clade of reptiles. Lizards differ
from snakes by having four limbs, eyelids, and external ears, which are
lacking in snakes. Lizard species range in size from chameleons and geckos
that are a few centimeters in length to the Komodo dragon, which is about 3
meters in length.
Snakes are thought to have descended from either burrowing lizards or
aquatic lizards over 100 million years ago ([{link]c). Snakes comprise about
3,000 species and are found on every continent except Antarctica. They
range in size from 10 centimeter-long thread snakes to 7.5 meter-long
pythons and anacondas. All snakes are carnivorous and eat small animals,
birds, eggs, fish, and insects.
Turtles are members of the clade Testudines (“having a shell”) ({link]d).
Turtles are characterized by a bony or cartilaginous shell, made up of the
carapace on the back and the plastron on the ventral surface, which
develops from the ribs. Turtles arose approximately 200 million years ago,
predating crocodiles, lizards, and snakes. Turtles lay eggs on land, although
many species live in or near water. Turtles range in size from the speckled
padloper tortoise at 8 centimeters (3.1 inches) to the leatherback sea turtle at
200 centimeters (over 6 feet). The term “turtle” is sometimes used to
describe only those species of Testudines that live in the sea, with the terms
“tortoise” and “terrapin” used to refer to species that live on land and in
fresh water, respectively.
Birds
Fossil and genomic data now suggest that birds belong within the reptile
clade, but they display a number of unique adaptations that set them apart.
Unlike the reptiles, birds are endothermic, meaning they generate their own
body heat through metabolic processes. The most distinctive characteristic
of birds is their feathers, which are modified reptilian scales. Birds have
several different types of feathers that are specialized for specific functions,
like contour feathers that streamline the bird’s exterior and loosely
structured down feathers that insulate ([link]a). Current thinking is that
some dinosaurs (the ancestors of modern birds) were also endothermic.
Feathers not only permitted the earliest birds to glide, and ultimately engage
in flapping flight, but they insulated the bird’s body, assisting the
maintenance of endothermy, even in cooler temperatures. Powering a flying
animal requires economizing on the amount of weight carried. As body
weight increases, the muscle output and energetic cost required for flying
increase. Birds have made several modifications to reduce body weight,
including hollow or pneumatic bones ([link]b) with air spaces that may be
connected to air sacs and cross-linked struts within their bones to provide
structural reinforcement. Parts of the vertebral skeleton and braincase are
fused to increase its strength while lightening its weight. Most species of
bird only possess one ovary rather than two, and no living birds have teeth
in their jaw, further reducing body mass.
Primary
feathers
Secondary
feathers
att xe)
Nal New
(a)
(a) Primary feathers are located at the wing tip and
provide thrust; secondary feathers are located close to
the body and provide lift. (b) Many birds have hollow
pneumatic bones, which make flight easier.
Birds possess a system of air sacs branching from their primary airway that
divert the path of air so that it passes unidirectionally through the lung,
during both inspiration and expiration. Unlike mammalian lungs in which
air flows in two directions as it is breathed in and out, air flows
continuously through the bird’s lung to provide a more efficient system of
gas exchange.
Mammals
Mammals are vertebrates that have hair and mammary glands used to
provide nutrition for their young. Certain features of the jaw, skeleton, skin,
and internal anatomy are also unique to mammals. The presence of hair is
one of the key characteristics of a mammal. Although it is not very
extensive in some groups, such as whales, hair has many important
functions for mammals. Mammals are endothermic, and hair provides
insulation by trapping a layer of air close to the body to retain metabolic
heat. Hair also serves as a sensory mechanism through specialized hairs
called vibrissae, better known as whiskers. These attach to nerves that
transmit touch information, which is particularly useful to nocturnal or
burrowing mammals. Hair can also provide protective coloration.
The skeletal system of mammals possesses unique features that differentiate
them from other vertebrates. Most mammals have heterodont teeth,
meaning they have different types and shapes of teeth that allow them to
feed on different kinds of foods. These different types of teeth include the
incisors, the canines, premolars, and molars. The first two types are for
cutting and tearing, whereas the latter two types are for crushing and
grinding. Different groups have different proportions of each type,
depending on their diet. Most mammals are also diphyodonts, meaning they
have two sets of teeth in their lifetime: deciduous or “baby” teeth, and
permanent teeth. In other vertebrates, the teeth can be replaced throughout
life.
Modern mammals are divided into three broad groups: monotremes,
marsupials, and eutherians (mammals with a placenta). The eutherians and
the marsupials collectively are called therian mammals, whereas
monotremes are called metatherians.
There are three living species of monotremes: the platypus and two species
of echidnas, or spiny anteaters (({link]). The platypus and one species of
echidna are found in Australia, whereas the other species of echidna is
found in New Guinea. Monotremes are unique among mammals, as they lay
leathery eggs, similar to those of reptiles, rather than giving birth to live
young. However, the eggs are retained within the mother’s reproductive
tract until they are almost ready to hatch. Once the young hatch, the female
begins to secrete milk from pores in a ridge of mammary tissue along the
ventral side of her body. Like other mammals, monotremes are endothermic
but regulate body temperatures somewhat lower (90 °F, 32 °C) than
placental mammals do (98 °F, 37 °C).
The platypus (left), a monotreme, possesses a leathery
beak and lays eggs rather than giving birth to live young.
An echidna, another monotreme, is shown in the right
photo. (credit “echidna”: modification of work by Barry
Thomas)
Marsupials are found primarily in Australia and nearby islands, although
about 100 species of opossums and a few species of two other families are
found in the Americas. Australian marsupials number over 230 species and
include the kangaroo, koala, bandicoot, and Tasmanian devil ({link]). Most
species of marsupials possess a pouch in which the young reside after birth,
receiving milk and continuing to develop. Before birth, marsupials have a
less complex placental connection, and the young are born much less
developed than in placental mammals.
The Tasmanian devil is one of several
marsupials native to Australia. (credit:
Wayne McLean)
Eutherian Diversity
(d)
Four eutherian mammals: A. A chiropteran, the Mexican Long-
tongued Bat (Choeronycteris mexicana) feeding on sugar water at a
hummingbird feeder. These bats pollinate many varieties of cactuses
and agaves, including the blue agave that is used to make tequila. B.
Pink River Dolphin (Inia geoffrensis), a freshwater cetacean found in
the Amazon River and its tributaries. C. A xenarthran, the Giant
Anteater or Tamandua (Tamandua tetradactyla), hunting for termites
in the Pantanal of Brazil. D. A member of the order Carnivora, the
Domestic Cat (Felis catus). Photo credits - David A. Rintoul
Eutherians are the most widespread of the mammals, occurring throughout
the world. There are several groups of eutherians, including Insectivora, the
insect eaters; Xenarthra, the toothless anteaters; Rodentia, the rodents;
Chiroptera, the bats; Cetacea, the aquatic mammals including whales;
Carnivora, carnivorous mammals including dogs, cats, and bears; and
Primates, which includes humans. Eutherian mammals are sometimes
called placental mammals, because all species have a complex placenta that
connects a fetus to the mother, allowing for gas, fluid, waste, and nutrient
exchange. While other mammals may possess a less complex placenta or
briefly have a placenta, all eutherians have a complex placenta during
gestation.
Homeostasis
"The constant conditions which are maintained in the body might be termed
equilibria. That word, however, has come to have a fairly exact meaning as
applied to relatively simple physico-chemical states, in closed systems,
where known forces are balanced. The coordinated physiological processes
which maintain most of the steady states in the organism are so complex,
and so peculiar to living beings - involving, as they may, the brain and
nerves, the heart, lungs, kidneys and spleen, all working cooperatively - that
I have suggested a special designation for these states: homeostasis. The
word does not imply something set and immobile, a stagnation. It means a
condition - a condition which may vary, but which is relatively constant."
Walter Cannon, The Wisdom of the Body, 1932, p. 24.
Cannon was an American physiologist who coined and popularized the
concept of homeostasis to describe the observations that animals could
maintain stable internal body conditions even when the external conditions
changed. Animal organs and organ systems constantly adjust to internal and
external changes through a process called homeostasis (“steady state”).
These changes might be in the level of glucose or calcium in blood or in
external temperatures. Homeostasis means to maintain dynamic
equilibrium in the body. It is dynamic because it is constantly adjusting to
the changes that the body’s systems encounter. It is equilibrium because
body functions are kept within specific ranges. Even an animal that is
apparently inactive is maintaining this homeostatic equilibrium.
Homeostatic Process
The goal of homeostasis is the maintenance of equilibrium around a point
or value called a set point. While there are normal fluctuations from the set
point, the body’s systems will usually attempt to go back to this point. A
change in the internal or external environment is called a stimulus and is
detected by a receptor; the response of the system is to adjust the parameter
toward the set point. For instance, if the body becomes too warm,
adjustments are made to cool the animal. If blood glucose concentration
rises after a meal, adjustments are made to lower the blood glucose level,
increasing uptake of glucose from blood into various tissues where it can be
converted to storage products like glycogen or triglyceride.
Control of Homeostasis
When a change occurs in an animal’s environment, an adjustment must be
made. The receptor senses the change in the environment, then sends a
signal to the control center (in most cases, the brain) which in turn
generates a response that is signaled to an effector. The effector is a muscle
(that contracts or relaxes) or a gland that secretes. Homeostatsis is
maintained by negative feedback loops. Positive feedback loops actually
push the organism further out of homeostasis, but may be necessary for life
to occur. Homeostasis is controlled by the nervous and endocrine system of
mammals, as described by Cannon in the 1930's.
Negative Feedback Mechanisms
Any homeostatic process that changes the direction of the stimulus is a
negative feedback loop. It can either cause an increase, or a decrease, in
the level of the stimulus that triggered the response, In all cases the
response is in the opposite direction of the change in the stimulus. In other
words, if a level is too high, the body does something to bring it down, and
conversely, if a level is too low, the body does something to make it go up.
Hence the term negative feedback. An example is animal maintenance of
blood glucose levels, as mentioned above. When an animal has eaten, blood
glucose levels rise. This is sensed by the nervous system. Specialized cells
in the pancreas sense this, and the hormone insulin is released by the
endocrine system. Insulin causes blood glucose levels to decrease, as would
be expected in a negative feedback system, as illustrated in [link]. However,
if an animal has not eaten and blood glucose levels decrease, this is sensed
in another group of cells in the pancreas, and the hormone glucagon is
released, causing glucose levels to increase. This is still a negative feedback
loop, which is defined as a situation where a change in one direction is
countered by a response in the opposite direction. Negative feedback loops
are the predominant mechanism used in homeostasis.
car & %
a
—
Ts
rd
Food is consumed and digested
In response to the lower causing blood level glucose to rise. In response to higher glucose
concentration of glucose, the levels, the pancreas secretes
pancreas stops secreting insulin. insulin into the blood.
In response to higher insulin levels,
glucose is transported into cells
and liver cells store glucose as
glycogen. As a result, glucose
levels drop.
Blood sugar levels are controlled by a negative feedback
loop. (credit: modification of work by Jon Sullivan)
Positive Feedback Loop
A positive feedback loop maintains the direction of the stimulus, possibly
accelerating it. Few examples of positive feedback loops exist in animal
bodies, but one is found in the cascade of chemical reactions that result in
blood clotting, or coagulation. As one clotting factor is activated, it
activates the next factor in sequence until a fibrin clot is achieved. The
direction is maintained, not changed, so this is positive feedback. Another
example of positive feedback is uterine contractions during childbirth, as
illustrated in [link]. The pituitary hormone oxytocin stimulates the
contraction of the uterus. This produces pain, which is sensed by the
nervous system. Instead of lowering the oxytocin and causing the pain to
subside, the nervous system causes the pituitary to secrete more oxytocin,
stimulating stronger contractions until the contractions are powerful enough
to produce childbirth.
The baby pushes
against the cervix,
causing it to stretch.
Stretching of the
\ \|) cervix causes
'// nerve impulses
to be sent to
the brain.
Oxytocin causes le . 2
the uterus to = ok'=
contract.
The brain stimulates
the pituitary to release
oxytocin.
The birth of a human infant
is the result of positive
feedback.
Set Point
It is possible to adjust a system’s set point, i.e., the level around which the
parameter of interest fluctuates.. When this happens, the feedback loop
works to maintain the new setting. An example of this is blood pressure:
over time, the normal or set point for blood pressure can increase as a result
of continued increases in blood pressure. The body no longer recognizes the
elevation as abnormal and no attempt is made to return to the lower set
point. The result is the maintenance of an elevated blood pressure that can
have harmful effects on the body. Medication can lower blood pressure and
lower the set point in the system to a more healthy level.
Changes can be made in a group of body organ systems in order to maintain
a set point in another system. This is called acclimatization. This occurs, for
instance, when an animal migrates to a higher altitude than it is accustomed
to. In order to adjust to the lower oxygen levels at the new altitude, the body
increases the number of red blood cells circulating in the blood to ensure
adequate oxygen delivery to the tissues. Another example of
acclimatization is animals that have seasonal changes in their coats: a
heavier coat in the winter ensures adequate heat retention, and a light coat
in summer assists in keeping body temperature from rising to harmful
levels.
Homeostasis: Thermoregulation
Body temperature affects body activities. Generally, as body temperature
rises, enzyme activity rises as well. For every ten degree centigrade rise in
temperature, enzyme activity doubles, up to a point. Body proteins,
including enzymes, begin to denature and lose their function at even higher
temperatures, as you learned in a previous module. Enzyme activity will
also decrease by half for every ten degree centigrade drop in temperature, to
the point of freezing, with a few exceptions. Some fish can withstand
freezing solid and return to normal with thawing, and one mammal (the
Arctic ground squirrel Urocitellus parryii) can lower its body temperature
to -3° C during its winter hibernation.
Endotherms and Ectotherms
Animals can be divided into two groups: some maintain a constant body
temperature in the face of differing environmental temperatures, while
others have a body temperature that is the same as their environment, and
thus varies with the environment. Animals that do not control their body
temperature are ectotherms. This group has been called cold-blooded, but
the term may not apply to an animal in the desert with a very warm body
temperature. In contrast to ectotherms, which rely on external temperatures
to set their body temperatures, poikilotherms are animals with constantly
varying internal temperatures. An animal that maintains a constant body
temperature in the face of environmental changes is called an endotherm.
Endotherms are animals that rely on internal sources for body temperature
but which can exhibit extremes in temperature. These animals are able to
maintain a level of activity at cooler temperature, whereas an ectotherm
cannot.
Heat can be exchanged between an animal and its environment through four
mechanisms: radiation, evaporation, convection, and conduction ((link]).
Radiation is the emission of electromagnetic “heat” waves. Heat comes
from the sun in this manner and radiates from dry skin the same way. Heat
can be removed with liquid from a surface during evaporation. This occurs
when a Mammal sweats. Convection currents of air remove heat from the
surface of dry skin as the air passes over it. Heat will be conducted from
one surface to another during direct contact with the surfaces, such as an
animal resting on a warm rock.
(a) Radiation (b) Evaporation
(c) Convection (d) Conduction
Heat can be exchanged by four mechanisms: (a)
radiation, (b) evaporation, (c) convection, or (d)
conduction. (credit b: modification of work by
“Kullez”/Flickr; credit c: modification of work by
Chad Rosenthal; credit d: modification of work by
“stacey.d”/Flickr)
Neural Control of Thermoregulation
The nervous system is important to thermoregulation, as illustrated in
[link]. The processes of homeostasis and temperature control are centered in
the hypothalamus of the advanced animal brain.
Body temperature falls Body temperature rises
Blood vessels constrict
so that heat is conserved.
Sweat glands do not
secrete fluid. Shivering
Blood vessels dilate,
resulting in heat loss to the
environment. Sweat glands
secrete fluid. As the fluid
evaporates, heat is lost
from the body.
Normal body
( temperature
. . DP XQ Heat is lost to
The body is able to regulate temperature
in response to signals from the nervous
system.
(involuntary contraction of
muscles) generates heat,
which warms the body.
The hypothalamus maintains the set point for body temperature through
reflexes that cause vasodilation and sweating when the body is too warm, or
vasoconstriction and shivering when the body is too cold. It responds to
chemicals from the body. When a bacterium is destroyed by phagocytic
leukocytes, chemicals called endogenous pyrogens (pyr=fire and genein=to
produce) are released into the blood. These chemicals circulate to the
hypothalamus and reset the thermostat. This allows the body’s temperature
to increase in what is commonly called a fever. An increase in body
temperature causes iron to be conserved, inhibiting bacterial division since
iron is an essential nutrient for bacteria. An increase in body heat also
increases the activity of the animal’s enzymes and protective cells while
inhibiting the enzymes and activity of the invading microorganisms.
Finally, heat itself may also kill the pathogen. Thus, a fever that was once
thought to be a complication of an infection, is now understood to be a
normal defense mechanism.
Digestive Systems
"If you were to open up a baby's head - and I am not for a moment
suggesting that you should - you would find nothing but an enormous drool
gland." - Dave Barry
The salivary glands (aka "drool glands") of vertebrates are just one part of
the elaborate and integrated organ system we call the digestive system. The
digestive system allows organisms, such as us, to obtain their nutrition from
the consumption of other organisms. Depending on their diet, animals can
be classified into the following categories: plant eaters (herbivores), meat
eaters (carnivores), and those that eat both plants and animals (omnivores).
The nutrients and macromolecules present in food are not immediately
accessible to the cells. There are a number of processes that modify food
within the animal body in order to make the nutrients and organic molecules
accessible for cellular function. As animals evolved in complexity of form
and function, their digestive systems (including the drool glands) have also
evolved to accommodate their various dietary needs.
Herbivores, Omnivores, and Carnivores
Herbivores are animals whose primary food source is plant-based.
Examples of herbivores, as shown in [link] include vertebrates like deer,
koalas, and some bird species, as well as invertebrates such as crickets and
caterpillars. These animals have evolved digestive systems capable of
handling large amounts of plant material. Herbivores can be further
classified into frugivores (fruit-eaters), granivores (seed eaters), nectivores
(nectar feeders), and folivores (leaf eaters).
Herbivores, like this (a) American Bison and
(b) Pipevine Swallowtail caterpillar, eat
primarily plant material. (photo credit: David
A. Rintoul)
Carnivores are animals that eat other animals. The word carnivore is
derived from Latin and literally means “meat eater.” Wild cats such as lions,
shown in [link]a and tigers are examples of vertebrate carnivores, as are
snakes and sharks, while invertebrate carnivores include sea stars, spiders,
and ladybugs, shown in [link]b. Obligate carnivores are those that rely
entirely on animal flesh to obtain their nutrients; examples of obligate
carnivores are members of the cat family, such as lions and cheetahs.
Facultative carnivores are those that also eat non-animal food in addition to
animal food. Note that there is no clear line that differentiates facultative
carnivores from omnivores; dogs would be considered facultative
carnivores.
(b)
Carnivores like the (a) lion eat primarily meat. The
(b) ambush bug is also a carnivore that consumes
small insects such as flies. (credit a: modification of
work by Kevin Pluck; credit b: David A. Rintoul)
Omnivores are animals that eat both plant- and animal-derived food. In
Latin, omnivore means to eat everything. Humans, bears (shown in [link]a),
and chickens are example of vertebrate omnivores; invertebrate omnivores
include cockroaches and crayfish (shown in [link]b).
Omnivores like the (a) bear and (b) crayfish eat both
plant and animal based food. (credit a: modification
of work by Dave Menke; credit b: modification of
work by Jon Sullivan)
Types of Digestive Systems
There re two types of digestive systems: incomplete and complete. An
incomplete digestive system has only one opening to the digestive tract
[link]a. Ingested food and excreted waste products pass through the same
opening. Incomplete digestive systems are found in Cnidarians and
Flatworms. The other type is, naturally, called a complete digestive
system, and this type has two openings [link]b. Food is ingested through
one opening, and waste products are excreted through a separate opening.
This type of digestive system is found in all other phyla, including
vertebrates.
The advantage of a complete digestive system is that it allows animals to
feed continuously, without waiting for the residues of the previous meal to
be released from the digestive tract. It also allows specialization of regions
of the digestive tract, which means that different food types can be digested
more efficiently. A particular region along the digestive tract, with different
physical and chemical conditions, can be optimized for one type of nutrient
and other regions can be optimized for efficient metabolism of other types
of nutrients.
Invertebrate Digestive Systems
Invertebrates can have incomplete or complete digestive systems, as noted
above. An incomplete digestive system has a gastrovascular cavity and only
one opening for digestion. Platyhelminthes (flatworms), Ctenophora (comb
jellies), and Cnidaria (coral, jelly fish, and sea anemones) have this type of
digestive system. Gastrovascular cavities, as shown in [link]a, are typically
a blind tube or cavity with only one opening, the “mouth”, which also
serves as an “anus”. Ingested material enters the mouth and passes through
a hollow, tubular cavity. Cells within the cavity secrete digestive enzymes
that break down the food. The food particles are engulfed by the cells lining
the gastrovascular cavity.
A complete digestive system, with an alimentary canal [link]b, is a more
advanced system: it consists of one tube with a mouth at one end and an
anus at the other. Earthworms are an example of an animal with a complete
digestive system. Once the food is ingested through the mouth, it passes
through the esophagus and is stored in an organ called the crop; then it
passes into the gizzard where it is churned and digested. From the gizzard,
the food passes through the intestine, the nutrients are absorbed, and the
waste is eliminated as feces, called castings, through the anus.
(a) A gastrovascular cavity has a single opening through
which food is ingested and waste is excreted, as shown
in this hydra and in this jellyfish medusa. (b) An
alimentary canal has two openings: a mouth for ingesting
food, and an anus for eliminating waste, as shown in this
nematode.
Vertebrate Digestive Systems
Vertebrates have evolved more complex digestive systems to adapt to their
dietary needs. Some animals have a single stomach, while others have
multi-chambered stomachs. Birds have developed a digestive system
adapted to eating unmasticated food.
Monogastric: Single-chambered Stomach
As the word monogastric suggests, this type of digestive system consists of
one (“mono”) stomach chamber (“gastric”). Humans and many animals
have a monogastric digestive system as illustrated in [link]ab. The process
of digestion begins with the mouth and the intake of food. The teeth play an
important role in masticating (chewing) or physically breaking down food
into smaller particles. The enzymes present in saliva also begin to
chemically break down food. The esophagus is a long tube that connects the
mouth to the stomach. Using peristalsis, or wave-like smooth muscle
contractions, the muscles of the esophagus push the food towards the
stomach. In order to speed up the actions of enzymes in the stomach, the
stomach is an extremely acidic environment, with a pH between 1.5 and
2.5. The gastric juices, which include enzymes in the stomach, act on the
food particles and continue the process of digestion. Further breakdown of
food takes place in the small intestine where enzymes produced by the liver,
the small intestine, and the pancreas continue the process of digestion. The
nutrients are absorbed into the blood stream across the epithelial cells lining
the walls of the small intestines. The waste material travels on to the large
intestine where water is absorbed and the drier waste material is compacted
into feces; it is stored until it is excreted through the rectum.
Esophagus
Liver Stomach Liver
Stomach
Pancreas
Small intestine
Pancreas Small intestine
Cecum
Cecum
Large intestine
(a) Human digestive system (b) Rabbit digestive system
(a) Humans and herbivores, such as the (b) rabbit, have a
monogastric digestive system. However, in the rabbit the
small intestine and cecum are enlarged to allow more
time to digest plant material. The enlarged organ
provides more surface area for absorption of nutrients.
Rabbits digest their food twice: the first time food passes
through the digestive system, it collects in the cecum,
and then it passes as soft feces called cecotrophes. The
rabbit re-ingests these cecotrophes to further digest them.
Avian
Birds face special challenges when it comes to obtaining nutrition from
food. Due to the constraints imposed by having to be lightweight in order to
fly, they have lost some adaptations found in their dinosaur ancestors. For
example, they do not have teeth, and so their digestive system, shown in
[link], must be able to process un-masticated food. Birds have evolved a
variety of beak types that reflect the vast variety in their diet, ranging from
seeds and insects to fruits and nuts. Because most birds fly, their metabolic
rates are high in order to efficiently process food and keep their body
weight low. The stomach of birds has two chambers: the proventriculus,
where gastric juices are produced to digest the food before it enters the
stomach, and the gizzard, where the food is stored, soaked, and
mechanically ground. The undigested material forms food pellets that are
sometimes regurgitated. Most of the chemical digestion and absorption
happens in the intestine and the waste is excreted through the cloaca.
pW
lie :
Esophagus
Crop
Liver Proventriculus
Gizzard
Pancreas
Small intestine
Large intestine
Caeca
Cloaca
The avian esophagus has a
pouch, called a crop, which
stores food. Food passes from
the crop to the first of two
stomachs, called the
proventriculus, which
contains digestive juices that
break down food. From the
proventriculus, the food
enters the second stomach,
called the gizzard, which
grinds food. Some birds
swallow stones or grit, which
are stored in the gizzard, to
aid the grinding process.
Birds do not have separate
openings to excrete urine and
feces. Instead, uric acid from
the kidneys is secreted into
the large intestine and
combined with waste from
the digestive process. This
waste is excreted through an
opening called the cloaca.
Note:
Evolution Connection
Avian Adaptations
Birds have a highly efficient, simplified digestive system. Recent fossil
evidence has shown that the evolutionary divergence of birds from other
land animals was characterized by streamlining and simplifying the
digestive system. Unlike many other animals, birds do not have teeth to
chew their food. In place of lips, they have sharp pointy beaks. Instead of
teeth, they have a proventricullus, or gizzard, for griding up food. The
emergence of these changes seems to coincide with the inclusion of seeds
in the bird diet. Seed-eating birds have beaks that are shaped for grabbing
seeds and the two-compartment stomach allows for delegation of tasks.
Since birds need to remain light in order to fly, passage time in the gut is
very short, which means they digest their food very quickly and need to eat
often. Contrast this with the ruminants, where the digestion of plant matter
takes a very long time and a heavy, water-filled digestive tract. What
would you predict would be some characteristics of birds that eat like a
cow, ingesting primarily leaves and shoots?
Ruminants
Ruminants are herbivores like cows, sheep, goats, bison, etc. whose entire
diet consists of eating large amounts of leaves and shoots. They have
evolved digestive systems that help them digest the vast amounts of
cellulose in this diet. An interesting feature of some ruminants mouths is
that they do not have upper incisor teeth. They use their lower teeth, tongue
and lips to tear and chew their food. From the mouth, the food travels to the
esophagus and on to the stomach.
To help digest the large amount of plant material, the stomach of the
ruminants is a multi-chambered organ, as illustrated in [link]. The four
compartments of the stomach are called the rumen, reticulum, omasum, and
abomasum. These chambers contain many microbes that break down
cellulose and ferment ingested food. The abomasum is the “true” stomach
and is the equivalent of the monogastric stomach chamber where gastric
juices are secreted. The four-compartment gastric chamber provides a larger
space and the microbial support necessary to digest plant material in
ruminants; it is essentially a bacterial fermentation vessel. The fermentation
process requires lots of watery fluid, and produces large amounts of gas in
the stomach chamber, which must be eliminated. As in other animals, the
small intestine plays an important role in nutrient absorption, and the large
intestine helps in the elimination of waste.
Large Small
intestine intestine
.
Anus
a) Reticulum
a
fe) u
masum , J)
Abomasum , a
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gt
Ruminant animals, such as goats and cows, have a four
chambered stomach. The first two chambers, the rumen and
the reticulum, contain prokaryotes and protists that are able
to digest cellulose fiber. The ruminant regurgitates cud
from the reticulum, chews it, and swallows it into a third
chamber, the omasum, which removes water. The cud then
passes onto the fourth chamber, the abomasum, where it is
digested by enzymes produced by the ruminant.
Parts of the Digestive System
The vertebrate digestive system is designed to facilitate the transformation
of food matter into the nutrient components that sustain organisms.
Oral Cavity
The oral cavity, or mouth, is the point of entry of food into the digestive
system, illustrated in [link]. The food consumed is broken into smaller
particles by mastication, the chewing action of the teeth. All mammals have
teeth and can chew their food.
The extensive chemical process of digestion begins in the mouth. As food is
being chewed, saliva, produced by the salivary glands, mixes with the food.
Saliva is a watery substance secreted by salivary glands into the mouths of
many animals. Saliva contains mucus that moistens food and buffers the pH
of the food. Saliva also contains immunoglobulins and lysozymes, which
have antibacterial action to reduce tooth decay by inhibiting growth of some
bacteria. Saliva also contains an enzyme called salivary amylase that begins
the process of converting starches in the food into a disaccharide called
maltose. The chewing and wetting action provided by the teeth and saliva
prepare the food into a mass called the bolus for swallowing. The tongue
helps in swallowing—moving the bolus from the mouth into the pharynx.
The pharynx opens to two passageways: the trachea, which leads to the
lungs, and the esophagus, which leads to the stomach. The trachea has an
opening called the glottis, which is covered by a cartilaginous flap called
the epiglottis. When swallowing, the epiglottis closes the glottis and food
passes into the esophagus and not the trachea. This arrangement allows
food to be kept out of the trachea and lungs.
Nasal cavity
Parotid gland
Teeth
Submandibular gland
Sublingual gland \
(a) (b)
Digestion of food begins in the (a) oral cavity. Food is
masticated by teeth and moistened by saliva secreted from
the (b) salivary glands. Enzymes in the saliva begin to
digest starches and fats. With the help of the tongue, the
resulting bolus is moved into the esophagus by swallowing.
(credit: modification of work by the National Cancer
Institute)
Esophagus
The esophagus is a tubular organ that connects the mouth to the stomach.
The chewed and softened food passes through the esophagus after being
swallowed. The smooth muscles of the esophagus undergo a series of wave-
like movements called peristalsis that push the food toward the stomach, as
illustrated in [link]. The peristalsic wave is unidirectional—it moves food
from the mouth to the stomach, and reverse movement is not possible. The
peristaltic movement of the esophagus is an involuntary reflex; it takes
place in response to the act of swallowing.
Direction
of food
The esophagus transfers food from
the mouth to the stomach through
peristaltic movements.
A ring-like muscle called a sphincter forms valves in the digestive system.
The gastro-esophageal sphincter is located at the stomach end of the
esophagus. In response to swallowing and the pressure exerted by the bolus
of food, this sphincter opens, and the bolus enters the stomach. When there
is no swallowing action, this sphincter is shut and prevents the contents of
the stomach from traveling up the esophagus. Many animals have a true
sphincter; however, in humans, there is no true sphincter, but the esophagus
remains closed when there is no swallowing action. Acid reflux or
“heartburn” occurs when the acidic digestive juices escape into the
esophagus.
Stomach
A large part of digestion occurs in the stomach, shown in [link]. The
stomach is a saclike organ that secretes gastric digestive juices. The pH in
the stomach is between 1.5 and 2.5. This highly acidic environment is
required for the chemical breakdown of food and the extraction of nutrients.
When empty, the stomach is a rather small organ; however, it can expand to
up to 20 times its resting size when filled with food. This characteristic is
particularly useful for animals that need to eat when food is available.
Liver
Stomach
Gallbladder
Pancreas
Colon
Transverse colon
Ascending colon
Descending colon
Cecum
Appendix
The human stomach has an extremely
acidic environment where most of the
protein gets digested. (credit:
modification of work by Mariana Ruiz
Villareal)
The stomach is also the major site for protein digestion in animals other
than ruminants. Protein digestion is mediated by an enzyme called pepsin in
the stomach chamber. Pepsin (secreted by cells in the stomach lining)
breaks peptide bonds and cleaves proteins into smaller polypeptides.
Another cell type—parietal cells—secrete hydrogen and chloride ions,
which combine in the lumen to form hydrochloric acid, the primary acidic
component of the stomach juices. The highly acidic environment also kills
many microorganisms in the food and, combined with the action of the
enzyme pepsin, results in the hydrolysis of protein in the food. Chemical
digestion is facilitated by the churning action of the stomach. Contraction
and relaxation of smooth muscles completely mixes the stomach contents
about every 20 minutes. The partially digested food and gastric juice
mixture is called chyme. Chyme passes from the stomach to the small
intestine. Further protein digestion takes place in the small intestine. Gastric
emptying occurs within two to six hours after a meal. Only a small amount
of chyme is released into the small intestine at a time. The movement of
chyme from the stomach into the small intestine is regulated by the pyloric
sphincter.
When digesting protein and some fats, the stomach lining must be protected
from getting digested by pepsin. There are two points to consider when
describing how the stomach lining is protected. Firstly, the enzyme pepsin
is synthesized in an inactive form (pepsinogen), which is activated by the
acid and other proteases in the stomach contents. This protects the cells
which secrete pepsin, because pepsinogen does not have the full enzyme
functionality of pepsin. Second, the stomach has a thick mucus lining that
protects the underlying tissue from the action of the digestive juices. When
this mucus lining is ruptured, ulcers can form in the stomach. Ulcers are
open wounds in or on an organ caused by bacteria (Helicobacter pylori)
when the mucus lining is ruptured and fails to reform.
Small Intestine
Chyme moves from the stomach to the small intestine. The small intestine
is the organ where the digestion of protein, fats, and carbohydrates is
completed. The small intestine is a long tube-like organ with a highly
folded surface containing finger-like projections called the villi. The apical
surface of each villus has many microscopic projections called microvilli.
These structures, illustrated in [link], are lined with epithelial cells on the
luminal side and allow for the nutrients to be absorbed from the digested
food and absorbed into the blood stream on the other side. The villi and
microvilli, with their many folds, increase the surface area of the intestine
and increase absorption efficiency of the nutrients. Most absorbed nutrients
(sugars, amino acids and nucleotides) in the blood are carried into the
hepatic portal vein, which leads to the liver. There, the liver regulates the
distribution of nutrients to the rest of the body and removes toxic
substances, including drugs, alcohol, and some pathogens. Fatty acids,
resulting from digestion of fat in the small intestine, do not enter the blood
stream directly, but are taken up by the lymphatic system in the small
intestine. These are eventually delivered to the blood via the thoracic duct,
to be metabolized by the liver as is the case for the other nutrients.
Absorptive cells
Microvilli
lan =
Muscle Villi
layers
‘ee
< 4] Fi 7
j
y
* Sn
Lymphatic vessel
Villi are folds on the small intestine lining that increase
the surface area to facilitate the absorption of nutrients.
The human small intestine is over 6m long and is divided into three parts:
the duodenum, the jejunum, and the ileum. The “C-shaped,” fixed part of
the small intestine is called the duodenum and is shown in [link]. The
duodenum is separated from the stomach by the pyloric sphincter which
opens to allow chyme to move from the stomach to the duodenum. In the
duodenum, chyme is mixed with pancreatic juices in an alkaline solution
rich in bicarbonate that neutralizes the acidity of chyme and acts as a buffer.
Pancreatic juices also contain several digestive enzymes. Digestive juices
from the pancreas, liver, and gallbladder, as well as from gland cells of the
intestinal wall itself, enter the duodenum. Bile is produced in the liver and
stored and concentrated in the gallbladder. Bile contains bile salts which
emulsify lipids while the pancreas produces enzymes that catabolize
starches, disaccharides, proteins, and fats. These digestive juices break
down the food particles in the chyme into glucose, triglycerides, and amino
acids. Some chemical digestion of food takes place in the duodenum.
Absorption of fatty acids into the lymphatic system also takes place in the
duodenum.
The second part of the small intestine is called the jejunum, shown in
[link]. Here, hydrolysis of nutrients is continued while most of the
carbohydrates and amino acids are absorbed through the intestinal lining.
The bulk of chemical digestion and nutrient absorption occurs in the
jejunum.
The ileum, also illustrated in [link] is the last part of the small intestine and
here the bile salts and vitamins are absorbed into blood stream. The
undigested food is sent to the colon from the ileum via peristaltic
movements of the muscle. The ileum ends and the large intestine begins at
the ileocecal valve. The vermiform, “worm-like,” appendix is located at the
ileocecal valve. The appendix of humans secretes no enzymes and has an
insignificant role in immunity.
Large Intestine
The large intestine, illustrated in [link], reabsorbs the water from the
undigested food material and processes the waste material. The human large
intestine is much smaller in length compared to the small intestine but
larger in diameter. It has three parts: the cecum, the colon, and the rectum.
The cecum joins the ileum to the colon and is the receiving pouch for the
waste matter. The cecum and colon are home to many trillions of bacteria or
“intestinal flora” that aid in the digestive processes. The colon can be
divided into four regions, the ascending colon, the transverse colon, the
descending colon and the sigmoid colon. The main functions of the colon
are to extract the water and mineral salts from undigested food, and to store
waste material. Carnivorous mammals have a shorter large intestine
compared to herbivorous mammals due to their diet.
Transverse
colon
Ascending
colon
Descending
colon
Cecum
Vermiform
: Sigmoid
appendix
colon
Rectum
The large intestine reabsorbs water
from undigested food and stores
waste material until it is
eliminated.
Rectum and Anus
The rectum is the terminal end of the large intestine, as shown in [link].
The primary role of the rectum is to store the feces until defecation. The
feces are propelled using peristaltic movements during elimination. The
anus is an opening at the far-end of the digestive tract and is the exit point
for the waste material. Two sphincters between the rectum and anus control
elimination: the inner sphincter is involuntary and the outer sphincter is
voluntary.
Accessory Organs
The organs discussed above are the organs of the digestive tract through
which food passes. Accessory organs are organs that add secretions
(enzymes) that catabolize food into nutrients. Accessory organs include
salivary glands, the liver, the pancreas, and the gallbladder. The liver,
pancreas, and gallbladder are regulated by hormones in response to the food
consumed.
The liver is the largest internal organ in humans and it plays a very
important role in digestion of fats and detoxifying blood. The liver produces
bile, a digestive juice that is required for the breakdown of fatty
components of the food in the duodenum. The liver also processes the
vitamins and fats and synthesizes many plasma proteins.
The pancreas is another important gland that secretes digestive juices. The
chyme produced from the stomach is highly acidic in nature; the pancreatic
juices contain high levels of bicarbonate, an alkali that neutralizes the acidic
chyme. Additionally, the pancreatic juices contain a large variety of
enzymes that are required for the digestion of protein and carbohydrates.
The gallbladder is a small organ that aids the liver by storing bile and
concentrating bile salts. When chyme containing fatty acids enters the
duodenum, the bile is secreted from the gallbladder into the duodenum.
Digestive System Processes
Introduction
" Every creature has its own food, and an appropriate alchemist with the task of dividing it ... The
alchemist takes the food and changes it into a tincture which he sends through the body to become
blood and flesh. This alchemist dwells in the stomach where he cooks and works. The man eats a
piece of meat, in which is both bad and good. When the meat reaches the stomach, there is the
alchemist who divides it. What does not belong to health he casts away to a special place, and
sends the good wherever it is needed." Philippus Aureolus Paracelsus, in Volumen Medicinae
Paramirum, c. 1520
Obtaining nutrition and energy from food is a multi-step process that, contrary to the thinking of
Paracelsus, does not involve alchemy or an alchemist. Many physical and biochemical processes
are involved in digestion of food, and it is also a highly regulated process For true animals, the
first step is ingestion, the act of taking in food. This is followed by digestion, absorption, and
elimination. In the following sections, each of these steps will be discussed in detail.
Ingestion
The large polymeric molecules found in intact food cannot pass through plasma membranes. So
these polymers need to be broken into smaller monomers so that animal cells can absorb and
metabolize them to produce energy. The first step in this process is ingestion. Ingestion is the
process of taking in food through the mouth. In vertebrates, the teeth, saliva, and tongue play
important roles in mastication (preparing the food into a bolus). While the food is being
mechanically broken down, the enzymes in saliva begin to chemically process the food as well.
The combined action of these processes modifies the food from large particles to a soft mass that
can be swallowed and can travel the length of the esophagus.
Digestion and Absorption
Digestion is the mechanical and chemical break down of food into small organic molecules. It is
important to break down macromolecules into smaller monomers that are of suitable size for
absorption across the digestive epithelium. Large, complex molecules (e.g., proteins,
polysaccharides, nucleic acids, and lipids) must be hydrolyzed into monomers before they can be
absorbed by the digestive epithelial cells. If this terminology seems a bit crazy, you may want to
review hydrolysis reactions [link] before proceeding. Different organs play specific roles in the
digestive process. The animal diet needs carbohydrates, protein, nucleic acids, and fat, as well as
vitamins and inorganic components for nutritional balance. We will briefly discuss digestion and
absorption of some of these in the sections below.
Carbohydrates
The digestion of carbohydrates begins in the mouth. The salivary enzyme amylase begins the
breakdown of food starches into maltose, a disaccharide. No significant further digestion of
carbohydrates takes place in the stomach. The esophagus produces no digestive enzymes but does
produce mucous for lubrication. The acidic environment in the stomach inhibits the action of the
salivary amylase enzyme.
The next step of carbohydrate digestion takes place in the duodenum. The chyme from the
stomach enters the duodenum and mixes with the digestive secretions from the pancreas, liver,
and gallbladder. Pancreatic juices also contain an amylase enzyme, which continues the
breakdown of starch and glycogen into maltose, a disaccharide. The disaccharides are broken
down into monosaccharides by enzymes called maltases, sucrases, and lactases, which are also
present in cells lining the small intestine. Maltase breaks down maltose into glucose. Other
disaccharides, such as sucrose and lactose are broken down by sucrase and lactase, respectively.
Sucrase breaks down sucrose (or “table sugar”) into glucose and fructose, and lactase breaks
down lactose (or “milk sugar’) into glucose and galactose. The monosaccharides (e.g., glucose
and fructose) thus produced are absorbed by the intestinal cells and transported into the
bloodstream. The steps in carbohydrate digestion are summarized in [link] and [link].
Polysaccharides
Amylase
Disaccharides
Maltase Sucrase Lactase
Monosaccharides Glucose + fructose Glucose + galactose
Digestion of carbohydrates is performed by several
enzymes. Starch and glycogen are broken down into glucose
by amylase and maltase. Sucrose (table sugar) and lactose
(milk sugar) are broken down by sucrase and lactase,
respectively.
me
Digestion of Carbohydrates
Produced Site of Substrate
Enzyme By Action Acting On End Products
Salivary amylase Sallvary Mouth Poly a onanies aul
er glands (Starch) s
oligosaccharides
Digestion of Carbohydrates
Produced Site of Substrate
Enzyme By Action Acting On End Products
: Small Polysaccharides Disacchonaes
Pancreatic amylase Pancreas ' . (maltose),
intestine (starch) :
monosaccharides
Lining of
the Monosaccharides
Oligosaccharidases ESUNE: lon Disaccharides (e.g., glucose,
brush intestine fructose,
border galactose)
membrane
Protein
A large part of protein digestion takes place in the stomach. The enzyme pepsin plays an
important role in the digestion of proteins by breaking down the intact protein to peptides, which
are short chains of four to nine amino acids. In the duodenum, other enzymes—trypsin, elastase,
and chymotrypsin—act on the peptides reducing them to smaller peptides. Trypsin elastase,
carboxypeptidase, and chymotrypsin are produced by the pancreas and released into the
duodenum where they act on the chyme. Further breakdown of peptides to single amino acids is
aided by enzymes called peptidases (those that break down peptides). Specifically,
carboxypeptidase, dipeptidase, and aminopeptidase play important roles in reducing the peptides
to free amino acids. The amino acids are absorbed into the bloodstream through the small
intestines. The steps in protein digestion are summarized in [link] and [link].
The liver regulates
distribution of
amino acids to the
rest of the body.
In the stomach,
pepsin breaks
down proteins
into fragments,
called peptides.
Amino acids are
absorbed from the
small intestine into
the blood stream.
Protein-digesting
enzymes are
secreted from
the pancreas
into the small
intestine.
In the small
intestine, a variety
of enzymes break
large peptides
Asmall amount into smaller
of dietary protein peptides, and then
is lost in the feces. into individual
amino acids.
Protein digestion is a multistep process that
begins in the stomach and continues through
the intestines.
Digestion of Protein
Produced Site of
Enzyme By Action
Pepsin ae Stomach
chief cells
Trypsin
Elastase Pancreas
Chymotrypsin
Small
intestine
Substrate
Acting On End Products
Proteins Peptides
Proteins Peptides
Digestion of Protein
Produced Site of Substrate
Enzyme By Action Acting On End Products
' Small : Amino acids
Carboxypeptidase Pancreas iramotiae Peptides andl peptides
Pope pase pulls . sila Peptides Amino acids
Dipeptidase intestine intestine
Lipids
The bulk of lipid digestion occurs in the small intestine, via the action of pancreatic lipase. When
chyme enters the duodenum, it triggers a hormonal response resulting in the release of bile, which
is produced in the liver and stored in the gallbladder. Bile aids in the digestion of lipids, primarily
triglycerides, by emulsification. Emulsification is a physical process in which large lipid globules
are dispersed into several small lipid globules. Lipids are hydrophobic substances: in the presence
of water, they will aggregate to form large globules to minimize exposure to water. These small
globules have a larger surface-to-volume ratio and thus an increased surface area for the lipases to
interact with. Bile contains bile salts, which are amphipathic, meaning they contain hydrophobic
and hydrophilic parts. Thus, the bile salts hydrophilic side can interface with water on one side
and the hydrophobic side interfaces with lipids on the other. By doing so, bile salts emulsify large
lipid globules into small lipid globules.
By forming an emulsion, bile salts increase the available surface area of the lipid particles
significantly. The pancreatic lipases can then act on the lipids more efficiently and digest them, as
detailed in [link]. Lipases break down the dietary triglycerides into fatty acids and monoglycerides
(one fatty acid attached to a glycerol molecule). These molecules can pass through the plasma
membrane of the cell and enter the epithelial cells of the intestinal lining. Lipase products (fatty
acids and monoglycerides) pass through the intestinal cells where they are reassembled into
triglycerides, and then are combined with proteins to form large fatty complexes called
chylomicrons. Chylomicrons contain triglycerides, cholesterol, and other lipids and have proteins
on their surface. The surface is also composed of the hydrophilic phosphate "heads" of
phospholipids. Together, they enable the chylomicron to move in an aqueous environment without
exposing the lipids to water. Chylomicrons leave the absorptive cells via exocytosis.
Chylomicrons enter the lymphatic vessels, and then enter the blood via the thoracic duct on their
way to the liver.
1. Lipids are emulsified
by the bile.
<a
muision
Lumen of XE
intestine
ag 3
Absorptive X% 74
epithelial cell i
Lymphatic
capillary
(a)
2.
Lipases break
down triglycerides
into fatty acids and
monoglycerides.
Fatty acids and
monoglycerides
are packaged into
micelles that are
absorbed by
microvilli.
. Fatty acids and
monoglycerides
are converted
back into
triglycerides.
The triglycerides
aggregate with
cholesterol,
proteins, and
phospholipids to
form chylomicrons.
. The chylomicrons
move into a lymph
capillary, which
transports them to
the rest of the body.
Triglyceride (fat)
Monoglyceride
Lipase
+
(b)
Lipids are digested and absorbed in the small intestine.
Summary of Digestion
+ Mechanical digestion (chewing
and swallowing)
* Chemical digestion of
carbohydrates
* Mechanical digestion (peristaltic
mixing and propulsion)
+ Chemical digestion of proteins
+ Absorption of lipid-soluble
substances, such as aspirin
Esophagus
Liver
Gallbladder ; ; . ici
* Mechanical digestion (mixing
y and propulsion, primarily
Pylorus g by segmentation)
* Chemical digestion of
carbohydrates, lipids, proteins,
and nucleic acids
* Absorption of peptides, amino
acids, glucose, fructose, lipids,
water, minerals, and vitamins
Pancreas
+ Mechanical digestion
(segmental mixing, mass
movement for propulsion)
* No chemical digestion except
by bacteria
+ Absorption of ions, water,
minerals, vitamins, and small
organic molecules produced
by bacteria
Rectum
Anal sphincters
Mechanical and chemical digestion of
food takes place in many steps, beginning
in the mouth and ending in the rectum.
Elimination
The final step in digestion is the elimination of undigested food content and waste products. The
undigested food material enters the colon, where most of the water is reabsorbed. Recall that the
colon is also home to the microflora called “intestinal flora” that aid in the digestion process. The
semi-solid waste is moved through the colon by peristaltic movements of the muscle and is stored
in the rectum. As the rectum expands in response to storage of fecal matter, it triggers the neural
signals required to set up the urge to eliminate. The solid waste is eliminated through the anus
using peristaltic movements of the rectum.
Nutrition
"Tell me what you eat: I will tell you what you are." Jean-Anthelme Brillat-
Savarin, The Philosopher in the Kitchen, Aphorism IV, 1825
Brillat-Savarin's aphorism may not be entirely true, but it holds a grain of
truth. Given the diversity of animal life on our planet, it is not surprising that
the animal diet would also vary substantially. The animal diet is the source of
materials needed for building DNA and other complex molecules needed for
growth, maintenance, and reproduction; collectively these processes are
called biosynthesis. The diet is also the source of materials for ATP
production in the cells. The diet must be balanced to provide the minerals and
vitamins that are required for cellular function.
Food Requirements
What are the fundamental requirements of the animal diet? The animal diet
should be well balanced and provide nutrients required for bodily function
and the minerals and vitamins required for maintaining structure and
regulation necessary for good health and reproductive capability. These
requirements for a human are illustrated graphically in [link]
Vegetables ry
Choose Ov
For humans, a balanced diet
includes fruits, vegetables,
grains, and protein. (credit:
USDA)
Note:
Everyday Connection
Let’s Move! Campaign
Obesity is a growing epidemic and the rate of obesity among children is
rapidly rising in the United States. To combat childhood obesity and ensure
that children get a healthy start in life, first lady Michelle Obama has
launched the Let’s Move! campaign. The goal of this campaign is to educate
parents and caregivers on providing healthy nutrition and encouraging active
lifestyles to future generations. This program aims to involve the entire
community, including parents, teachers, and healthcare providers to ensure
that children have access to healthy foods—more fruits, vegetables, and
whole grains—and consume fewer calories from processed foods. Another
goal is to ensure that children get physical activity. With the increase in
television viewing and stationary pursuits such as video games, sedentary
lifestyles have become the norm. Learn more at www.letsmove.gov.
Organic Precursors
The organic molecules required for building cellular material and tissues must
come from food. Carbohydrates or sugars are the primary source of organic
carbons in the animal body. During digestion, digestible carbohydrates are
ultimately broken down into glucose and used to provide energy through
metabolic pathways. Complex carbohydrates, including polysaccharides, can
be broken down into glucose through biochemical modification; however,
humans do not produce the enzyme cellulase and lack the ability to derive
glucose from the polysaccharide cellulose. In humans, these molecules
provide the fiber required for moving waste through the large intestine and a
healthy colon. The intestinal flora in the human gut are able to extract some
nutrition from these plant fibers. The excess sugars in the body are converted
into glycogen and stored in the liver and muscles for later use. Glycogen
stores are used to fuel prolonged exertions, such as long-distance running,
and to provide energy during food shortage. Excess glycogen can be
converted to fats, which are stored in the lower layer of the skin of mammals
for insulation and energy storage. Excess digestible carbohydrates are stored
by mammals in order to survive famine and aid in mobility.
Another important requirement is that of nitrogen. Protein catabolism
provides a source of organic nitrogen. Amino acids are the building blocks of
proteins and protein breakdown provides amino acids that are used for
cellular function. The carbon and nitrogen derived from these become the
building block for nucleotides, nucleic acids, proteins, cells, and tissues.
Excess nitrogen must be excreted as it is toxic. Fats add flavor to food and
promote a sense of satiety or fullness. Fatty foods are also significant sources
of energy because one gram of fat contains nine calories. Fats are required in
the diet to aid the absorption of fat-soluble vitamins and the production of fat-
soluble hormones.
Essential Nutrients
While the animal body can synthesize many of the molecules required for
function from the organic precursors, there are some nutrients that need to be
consumed from food. These nutrients are termed essential nutrients,
meaning they must be eaten, and the body cannot produce them.
The omega-3 alpha-linolenic acid and the omega-6 linoleic acid are essential
fatty acids needed to make some membrane phospholipids. Vitamins are
another class of essential organic molecules that are required in small
quantities for many enzymes to function and, for this reason, are considered
to be co-enzymes. Absence or low levels of vitamins can have a dramatic
effect on health, as outlined in [link] and [link]. Both fat-soluble and water-
soluble vitamins must be obtained from food. Minerals, listed in [link], are
inorganic essential nutrients that must be obtained from food. Among their
many functions, minerals help in structure and regulation and are considered
co-factors. Certain amino acids also must be procured from food and cannot
be synthesized by the body. These amino acids are the “essential” amino
acids. The human body can synthesize only 11 of the 20 required amino
acids; the rest must be obtained from food. The essential amino acids are
listed in [link].
Water-soluble Essential Vitamins
Vitamin
Vitamin By,
(Thiamine)
Vitamin Bo
(Riboflavin)
Function
Needed by the
body to process
lipids, proteins,
and
carbohydrates
Coenzyme
removes CO>
from organic
compounds
Takes an active
role in
metabolism,
aiding in the
conversion of
food to energy
(FAD and
FMN)
Deficiencies
Can Lead To
Muscle
weakness,
Beriberi:
reduced heart
function, CNS
problems
Cracks or sores
on the outer
surface of the
lips (cheliosis);
inflammation
and redness of
the tongue;
moist, scaly
skin
inflammation
(seborrheic
dermatitis)
Sources
Milk,
meat, dried
beans,
whole
grains
Meat,
eggs,
enriched
grains,
vegetables
Water-soluble Essential Vitamins
Vitamin
Vitamin Bz
(Niacin)
Vitamin Bs
(Pantothenic
acid)
Vitamin Bg
(Pyridoxine)
Function
Used by the
body to release
energy from
carbohydrates
and to process
alcohol;
required for the
synthesis of sex
hormones;
component of
coenzyme
NAD* and
NADP*
Assists in
producing
energy from
foods (lipids, in
particular);
component of
coenzyme A
The principal
vitamin for
processing
amino acids
and lipids; also
helps convert
nutrients into
energy
Deficiencies
Can Lead To
Pellagra, which
can result in
dermatitis,
diarrhea,
dementia, and
death
Fatigue, poor
coordination,
retarded
growth,
numbness,
tingling of
hands and feet
Irritability,
depression,
confusion,
mouth sores or
ulcers, anemia,
muscular
twitching
Sources
Meat,
eggs,
grains,
nuts,
potatoes
Meat,
whole
grains,
milk,
fruits,
vegetables
Meat,
dairy
products,
whole
grains,
orange
juice
Water-soluble Essential Vitamins
Vitamin
Vitamin B7
(Biotin)
Vitamin Bo
(Folic acid)
Vitamin B 12
(Cobalamin)
Function
Used in energy
and amino acid
metabolism, fat
synthesis, and
fat breakdown;
helps the body
use blood sugar
Assists the
normal
development of
cells, especially
during fetal
development;
helps
metabolize
nucleic and
amino acids
Maintains
healthy nervous
system and
assists with
blood cell
formation;
coenzyme in
nucleic acid
metabolism
Deficiencies
Can Lead To
Hair loss,
dermatitis,
depression,
numbness and
tingling in the
extremities;
neuromuscular
disorders
Deficiency
during
pregnancy is
associated with
birth defects,
such as neural
tube defects
and anemia
Anemia,
neurological
disorders,
numbness, loss
of balance
Sources
Meat,
eggs,
legumes
and other
vegetables
Leafy
green
vegetables,
whole
wheat,
fruits,
nuts,
legumes
Meat,
eggs,
animal
products
Water-soluble Essential Vitamins
Deficiencies
Vitamin Function Can Lead To Sources
ee rvy, which
Helps maintain eet y Citrus
results in
connective fruits,
bleeding, hair
Vitamin C tissue: bone, Sa Aon isc broccoli,
(Ascorbic cartilage, and ° : pas ‘ tomatoes,
acid) dentin; boosts om Yee and red sweet
the maine swelling; bell
Lee res delayed wound eee
y healing PEPP
Fat-soluble Essential Vitamins
Deficiencies
Can Lead
Vitamin Function To Sources
Fat-soluble Essential Vitamins
Vitamin
Vitamin A
(Retinol)
Vitamin D
Function
Critical to the
development
of bones,
teeth, and
skin; helps
maintain
eyesight,
enhances the
immune
system, fetal
development,
gene
expression
Critical for
calcium
absorption for
bone
development
and strength;
maintains a
stable nervous
system;
maintains a
normal and
strong
heartbeat;
helps in blood
clotting
Deficiencies
Can Lead
To
Night-
blindness,
skin
disorders,
impaired
immunity
Rickets,
osteomalacia,
immunity
Sources
Dark green
leafy
vegetables,
yellow-
orange
vegetables
fruits,
milk,
butter
Cod liver
oil, milk,
egg yolk
Fat-soluble Essential Vitamins
Vitamin
Vitamin E
(Tocopherol)
Vitamin K
(Phylloquinone)
A healthy diet should include a variety of
Function
Lessens
oxidative
damage of
cells,and
prevents lung
damage from
pollutants;
vital to the
immune
system
Essential to
blood clotting
Deficiencies
Can Lead
To
Deficiency is
rare; anemia,
nervous
system
degeneration
Bleeding and
easy bruising
Sources
Wheat
germ oil,
unrefined
vegetable
oils, nuts,
seeds,
grains
Leafy
green
vegetables,
tea
foods to ensure that needs for essential
nutrients are met. (credit: Keith Weller,
USDA ARS)
Minerals and Their Function in the Human Body
Mineral
*Calcium
* Chlorine
Function
Needed for
muscle and
neuron function;
heart health;
builds bone and
supports
synthesis and
function of blood
cells; nerve
function
Needed for
production of
hydrochloric acid
(HC]) in the
stomach and
nerve function;
osmotic balance
Deficiencies
Can Lead To
Osteoporosis,
rickets,
muscle
spasms,
impaired
growth
Muscle
cramps, mood
disturbances,
reduced
appetite
Sources
Milk,
yogurt,
fish, green
leafy
vegetables,
legumes
Table salt
Minerals and Their Function in the Human Body
Mineral
Copper
(trace
amounts)
Iodine
Iron
Function
Required
component of
many redox
enzymes,
including
cytochrome c
oxidase; cofactor
for hemoglobin
synthesis
Required for the
synthesis of
thyroid hormones
Required for
many proteins
and enzymes,
notably
hemoglobin, to
prevent anemia
Deficiencies
Can Lead To
Copper
deficiency is
rare
Goiter
Anemia,
which causes
poor
concentration,
fatigue, and
poor immune
function
Sources
Liver,
oysters,
cocoa,
chocolate,
sesame,
nuts
Seafood,
iodized
salt, dairy
products
Red meat,
leafy green
vegetables,
fish (tuna,
salmon),
eggs, dried
fruits,
beans,
whole
grains
Minerals and Their Function in the Human Body
Mineral
*Magnesium
Manganese
(trace
amounts)
Molybdenum
(trace
amounts)
*Phosphorus
Function
Required co-
factor for ATP
formation; bone
formation;
normal
membrane
functions; muscle
function
A cofactor in
enzyme
functions; trace
amounts are
required
Acts as a cofactor
for three essential
enzymes in
humans: sulfite
oxidase, xanthine
oxidase, and
aldehyde oxidase
A component of
bones and teeth;
helps regulate
acid-base
balance;
nucleotide
synthesis
Deficiencies
Can Lead To
Mood
disturbances,
muscle
spasms
Manganese
deficiency is
rare
Molybdenum
deficiency is
rare
Weakness,
bone
abnormalities,
calcium loss
Sources
Whole
grains,
leafy green
vegetables
Common
in most
foods
Milk, hard
cheese,
whole
grains,
meats
Minerals and Their Function in the Human Body
Mineral
*Potassium
Selenium
(trace
amounts)
*Sodium
Zinc (trace
amounts)
Function
Vital for muscles,
heart, and nerve
function
A cofactor
essential to
activity of
antioxidant
enzymes like
glutathione
peroxidase; trace
amounts are
required
Systemic
electrolyte
required for many
functions; acid-
base balance;
water balance;
nerve function
Required for
several enzymes
such as
carboxypeptidase,
liver alcohol
dehydrogenase,
and carbonic
anhydrase
Deficiencies
Can Lead To
Cardiac
rhythm
disturbance,
muscle
weakness
Selenium
deficiency is
rare
Muscle
cramps,
fatigue,
reduced
appetite
Anemia, poor
wound
healing, can
lead to short
stature
Sources
Legumes,
potato
skin,
tomatoes,
bananas
Common
in most
foods
Table salt
Common
in most
foods
Minerals and Their Function in the Human Body
Deficiencies
Mineral Function Can Lead To Sources
*Greater than 200mg/day required
Essential Amino Acids
Amino acids that must be Amino acids anabolized by the
consumed body
isoleucine alanine
leucine selenocysteine
lysine aspartate
methionine cysteine
phenylalanine glutamate
tryptophan glycine
valine proline
histidine* serine
threonine tyrosine
arginine* asparagine
Essential Amino Acids
Amino acids that must be Amino acids anabolized by the
consumed body
*The human body can synthesize histidine and arginine, but not in the
quantities required, especially for growing children.
The Circulatory System
Introduction
"Observation by means of the microscope will reveal more wonderful
things than those viewed in regard to mere structure and connection: for
while the heart is still beating the contrary (i.e., in opposite directions in the
different vessels) movement of the blood is observed in the vessels—though
with difficulty—so that the circulation of the blood is clearly exposed."
Marcello Malpighi, De Pulmonibus, 1661
Malpighi's work (mostly on frogs) outlined the finer microscopic details of
circulation, following the work of Harvey, who described the circulatory
system at a macroscopic level. In all animals, except a few simple types, the
circulatory system is used to transport nutrients and gases through the body.
Simple diffusion allows some water, nutrient, waste, and gas exchange into
primitive animals that are only a few cell layers thick; however, bulk flow is
the only method by which the entire body of larger more complex
organisms is accessed.
Circulatory System Architecture
The circulatory system is effectively a network of cylindrical vessels: the
arteries, veins, and capillaries that emanate from a pump, the heart. In all
vertebrate organisms, as well as some invertebrates, this is a closed system,
in which the blood is not free in a cavity. In a closed circulatory system,
blood is contained inside blood vessels and circulates unidirectionally from
the heart around the systemic circulatory route, then returns to the heart
again, as illustrated in [link]a. As opposed to a closed system, arthropods—
including insects, crustaceans, and most mollusks—have an open
circulatory system, as illustrated in [link]b. In an open circulatory system,
the fluid is not enclosed in the blood vessels but is pumped into a cavity
called a hemocoel; rather than blood, this fluid is called hemolymph
because the blood mixes with the interstitial fluid. As the heart beats and
the animal moves, the hemolymph circulates around the organs within the
body cavity and then reenters the hearts through openings called ostia. This
movement allows for gas and nutrient exchange. An open circulatory
system does not use as much energy as a closed system to operate or to
maintain; however, there is a trade-off with the amount of blood that can be
moved to highly metabolically active organs and tissues.
Dorsal blood vessel Hearts Ostia (openings in heart)
(main heart) :
Dorsal blood
vessel
Body cavity
Ventral blood vessel
(a) Closed circulatory system (b) Open circulatory system
In (a) closed circulatory systems, the heart pumps blood through
vessels that are separate from the interstitial fluid of the body.
Most vertebrates and some invertebrates, like this annelid
earthworm, have a closed circulatory system. In (b) open
circulatory systems, a fluid called hemolymph is pumped through
a blood vessel that empties into the body cavity. Hemolymph
returns to the blood vessel through openings called ostia.
Arthropods like this bee and most mollusks have open circulatory
systems.
Circulatory System Variation in Animals
The circulatory system varies from simple systems in invertebrates to more
complex systems in vertebrates. The simplest animals, such as the sponges
(Porifera) and rotifers (Rotifera), do not need a circulatory system because
diffusion allows adequate exchange of water, nutrients, and waste, as well
as dissolved gases, as shown in [link]a. Organisms that are more complex
but still only have two layers of cells in their body plan, such as jellies
(Cnidaria) and comb jellies (Ctenophora) also use diffusion through their
epidermis and internally through the gastrovascular compartment. Both
their internal and external tissues are bathed in an aqueous environment and
exchange fluids by diffusion on both sides, as illustrated in [link]b.
Exchange of fluids is assisted by the pulsing of the jellyfish body.
(a) Sponge (b) Jellyfish
Simple animals consisting of a single cell layer such as the (a)
sponge or only a few cell layers such as the (b) jellyfish do not
have a circulatory system. Instead, gases, nutrients, and wastes are
exchanged by diffusion.
For more complex organisms, diffusion is not efficient for moving gases,
nutrients, and waste effectively through the body; natural selection led to
the development of more efficient systems. Most arthropods and many
mollusks have open circulatory systems. In an open system, an elongated
beating heart pushes the hemolymph through the body, and muscle
contractions help to move fluids. The larger more complex crustaceans,
including lobsters, have developed arterial-like vessels to push blood
through their bodies, and the most active mollusks, such as squids, have
evolved a closed circulatory system and are able to move rapidly to catch
prey. Closed circulatory systems are found in all vertebrates; however, there
are significant differences in the structure of the heart and the circulation of
blood between the different vertebrate groups due to adaptation during
evolution and associated differences in anatomy. [link] illustrates the basic
circulatory systems of some vertebrates: fish, amphibians, reptiles, and
mammals.
Gill circulation
Gill
capillaries
Ventricle
Body
Systemic circulation capillaries
(a) Fish
Pulmonary circulation
Lung
capillaries
Left
atrium
= Septum
atrium
Right Left
ventricle ventricle
Body
capillaries
Systemic circulation
(c) Reptile
Pulmonary and
skin circulation
Lung and
skin capillaries
Right atrium Left atrium
Body capillaries Ventricle
Systemic circulation
(b) Amphibians
Pulmonary circulation
Left atrium
Lung
capillaries
Body capillaries
Right Ei 4Aev See Left
ventricle =< = ventricle
Systemic circulation
(d) Mammals
(a) Fish have the simplest circulatory systems of the vertebrates:
blood flows unidirectionally from the two-chambered heart
through the gills and then the rest of the body. (b) Amphibians
have two circulatory routes: one for oxygenation of the blood
through the lungs and skin, and the other to take oxygen to the rest
of the body. The blood is pumped from a three-chambered heart
with two atria and a single ventricle. (c) Reptiles also have two
circulatory routes; however, blood is only oxygenated through the
lungs. The heart is three chambered, but the ventricles are partially
separated so some mixing of oxygenated and deoxygenated blood
occurs except in crocodilians and birds. (d) Mammals and birds
have the most efficient heart with four chambers that completely
separate the oxygenated and deoxygenated blood; it pumps only
oxygenated blood through the body and deoxygenated blood to the
lungs.
As illustrated in [link]a Fish have a single circuit for blood flow and a two-
chambered heart that has only a single atrium and a single ventricle. The
atrium collects blood that has returned from the body, and the ventricle
pumps the blood to the gills where gas exchange occurs and the blood is re-
oxygenated; this is called the gill circulation. The blood then continues
through the rest of the body before arriving back at the atrium; this is called
the systemic circulation. This unidirectional flow of blood produces a
gradient of oxygenated to deoxygenated blood around the fish’s systemic
circuit. The result is a limit in the amount of oxygen that can reach some of
the organs and tissues of the body, reducing the overall metabolic capacity
of fish.
In amphibians, reptiles, birds, and mammals, blood flow is directed in two
circuits: one through the lungs and back to the heart, which is called the
pulmonary circulation, and the other throughout the rest of the body and
its organs including the brain (systemic circulation). In amphibians, gas
exchange also occurs through the skin during pulmonary circulation and is
referred to as pulmocutaneous circulation.
As shown in [link]b, amphibians have a three-chambered heart that has two
atria and one ventricle rather than the two-chambered heart of fish. The two
atria (superior heart chambers) receive blood from the two different circuits
(the lungs and the systems), and then there is some mixing of the blood in
the heart’s ventricle (inferior heart chamber), which reduces the oxygen
concentration in the blood pumped from the ventricle. The advantage to this
arrangement is that high pressure in the vessels pushes blood to the lungs
and body. The mixing is mitigated by a ridge within the ventricle that
diverts oxygen-rich blood through the systemic circulatory system and
deoxygenated blood to the pulmocutaneous circuit. For this reason,
amphibians are often described as having double circulation.
Most reptiles also have a three-chambered heart similar to the amphibian
heart that directs blood to the pulmonary and systemic circuits, as shown in
[link]c. The ventricle is divided more effectively by a partial septum, which
results in even less mixing of oxygenated and deoxygenated blood. Some
reptiles (alligators and crocodiles) are the most primitive animals to exhibit
a four-chambered heart. Crocodilians have a unique circulatory mechanism
where the heart shunts blood from the lungs toward the stomach and other
organs during long periods of submergence, for instance, while the animal
waits for prey or stays underwater waiting for prey to rot. One adaptation
includes two main arteries that leave the same part of the heart: one takes
blood to the lungs and the other provides an alternate route to the stomach
and other parts of the body. Two other adaptations include a hole in the
heart between the two ventricles, called the foramen of Panizza, which
allows blood to move from one side of the heart to the other, and
specialized connective tissue that slows the blood flow to the lungs.
Together these adaptations have made crocodiles and alligators one of the
most successful and ancient animal groups on earth.
In mammals and birds, the heart is also divided into four chambers: two
atria and two ventricles, as illustrated in [link]d. The oxygenated blood is
completely separated from the deoxygenated blood, which improves the
efficiency of double circulation and is probably required for the warm-
blooded lifestyle of mammals and birds. The four-chambered heart of birds
and mammals evolved independently from ancestors with a three-
chambered heart. The independent evolution of the same or a similar
biological trait is referred to as convergent evolution.
Components of Blood
Oxygen-binding proteins (hemoglobin, hemocyanin, etc.) are one of the
main components of blood in all animals. The blood is more than those
proteins, though. Blood is actually a term used to describe the liquid that
moves through the vessels and includes plasma (the liquid portion, which
contains water, proteins, salts, lipids, and glucose) and the cells (red and
white cells) and cell fragments called platelets. Plasma is actually the major
component of blood and contains the water, proteins, electrolytes, lipids,
and glucose. The cells are responsible for carrying the gases (red cells) and
immune the response (white). The platelets are responsible for blood
clotting. In humans, cellular components make up approximately 45 percent
of the blood and the liquid plasma 55 percent. Blood is 20 percent of a
human's extracellular fluid and eight percent of the weight of an average
human.
The Role of Blood in the Body
Blood, like the human blood illustrated in [link] is important for regulation
of the body’s systems and homeostasis. Blood helps maintain homeostasis
by stabilizing pH, temperature, osmotic pressure, and by eliminating excess
heat. Blood supports growth by distributing nutrients and hormones, and by
removing waste. Blood plays a protective role by transporting clotting
factors and platelets to prevent blood loss and transporting the disease-
fighting agents or white blood cells to sites of infection.
— Monocyte
Erythrocyte
en blood “|
Eosinophil ; = A
¥ Oe L)
The cells and cellular components of human blood are shown.
Red blood cells deliver oxygen to the cells and remove carbon
dioxide. White blood cells—including neutrophils, monocytes,
lymphocytes, eosinophils, and basophils—are involved in the
immune response. Platelets form clots that prevent blood loss
after injury.
Red Blood Cells
Red blood cells, or erythrocytes (erythro- = “red”; -cyte = “cell’”), are
specialized cells that circulate through the body delivering oxygen to cells;
they are generated by division of stem cells in the bone marrow. In
mammals, red blood cells are small biconcave cells that at maturity do not
contain a nucleus or mitochondria and are only 7—8 pm in size. In birds and
reptiles, erythrocytes have nuclie and mitochondria.
The red coloring of human blood comes from the iron-containing protein
hemoglobin, illustrated in [link]a. The principal job of these proteins is to
carry oxygen, but they also transports carbon dioxide as well. Hemoglobin
is packed into human red blood cells at a rate of about 250 million
molecules of hemoglobin per cell. Each hemoglobin molecule binds four
oxygen molecules so that each red blood cell carries one billion molecules
of oxygen. There are approximately 25 trillion red blood cells in the five
liters of blood in the human body, which could carry up to 25 sextillion (25
x 10°!) molecules of oxygen in the body at any time. In mammals, the lack
of organelles in erythrocytes leaves more room for the hemoglobin
molecules, and the lack of mitochondria also prevents use of the oxygen for
metabolic respiration.
Not all organisms use hemoglobin as the method of oxygen transport.
Invertebrates that utilize hemolymph rather than blood use different
pigments to bind to the oxygen. These pigments use copper or iron to the
oxygen. Invertebrates have a variety of other respiratory pigments.
Hemocyanin, a blue-green, copper-containing protein, illustrated in [link]b
is found in mollusks, crustaceans, and some of the arthropods.
Chlorocruorin, a green-colored, iron-containing pigment is found in four
families of polychaete tubeworms. Hemerythrin, a red, iron-containing
protein is found in some polychaete worms and annelids and is illustrated in
[link]c. Despite the name, hemerythrin does not contain a heme group and
its oxygen-carrying capacity is poor compared to hemoglobin.
Heme
(a) Hemoglobin (b) Hemocyanin (c) Hemerythrin
In most vertebrates, (a) hemoglobin delivers oxygen to the body
and removes some carbon dioxide. Hemoglobin is composed of
four protein subunits, two alpha chains and two beta chains, and a
heme group that has iron associated with it. The iron reversibly
associates with oxygen, and in so doing is oxidized from Fe2* to
Fe**. In most mollusks and some arthropods, (b) hemocyanin
delivers oxygen. Unlike hemoglobin, hemolymph is not carried in
blood cells, but floats free in the hemolymph. Copper instead of
iron binds the oxygen, giving the hemolymph a blue-green color.
In annelids, such as the earthworm, and some other invertebrates,
(c) hemerythrin carries oxygen. Like hemoglobin, hemerythrin is
carried in blood cells and has iron associated with it, but despite
its name, hemerythrin does not contain heme.
The small size and large surface area of red blood cells allows for rapid
diffusion of oxygen and carbon dioxide across the plasma membrane. In the
lungs, carbon dioxide is released and oxygen is taken in by the blood. In the
tissues, oxygen is released from the blood and carbon dioxide is bound for
transport back to the lungs.
White Blood Cells
White blood cells, also called leukocytes (leuko = white), make up
approximately one percent (by volume) of the cells in blood. The role of
white blood cells is very different than that of red blood cells, as you have
learned previously. They are primarily involved in the immune response to
identify and target pathogens, such as invading bacteria, viruses, and other
foreign organisms. White blood cells are formed continually; some only
live for hours or days, but some live for years.
The morphology of white blood cells differs significantly from red blood
cells. They have nuclei and do not contain hemoglobin. The different types
of white blood cells are identified by their microscopic appearance after
histologic staining, and each has a different specialized function. The two
main groups, both illustrated in [link] are the granulocytes, which include
the neutrophils, eosinophils, and basophils, and the agranulocytes, which
include the monocytes and lymphocytes.
Granulocytes contain granules in their cytoplasm; the agranulocytes are so
named because of the lack of granules in their cytoplasm. Some leukocytes
become macrophages that either stay at the same site or move through the
blood stream and gather at sites of infection or inflammation where they are
attracted by chemical signals from foreign particles and damaged cells.
Lymphocytes are the primary cells of the immune system and include B
cells, T cells, and natural killer cells. B cells destroy bacteria and inactivate
their toxins. They also produce antibodies. T cells attack viruses, fungi,
some bacteria, transplanted cells, and cancer cells. T cells attack viruses by
releasing toxins that kill the viruses. Natural killer cells attack a variety of
infectious microbes and certain tumor cells.
Platelets and Coagulation Factors
Blood must clot to heal wounds and prevent excess blood loss. Small cell
fragments called platelets (thrombocytes) are attracted to the wound site
where they adhere by extending many projections and releasing their
contents. These contents activate other platelets and also interact with other
coagulation factors, which convert fibrinogen, a water-soluble protein
present in blood serum into fibrin (a non-water soluble protein), causing the
blood to clot. Many of the clotting factors require vitamin K to work, and
vitamin K deficiency can lead to problems with blood clotting. Many
platelets converge and stick together at the wound site forming a platelet
plug (also called a fibrin clot), as illustrated in [link]b. The plug or clot lasts
for a number of days and stops the loss of blood. Platelets are formed from
the disintegration of larger cells called megakaryocytes, like that shown in
[link]a. For each megakaryocyte, 2000-3000 platelets are formed with
150,000 to 400,000 platelets present in each cubic millimeter of blood.
Each platelet is disc shaped and 2—4 ym in diameter. They contain many
small vesicles but do not contain a nucleus.
Fibrin clot
(b)
(a) Platelets are formed from large cells called megakaryocytes.
The megakaryocyte breaks up into thousands of fragments that
become platelets. (b) Platelets are required for clotting of the
blood. The platelets collect at a wound site in conjunction with
other clotting factors, such as fibrinogen, to form a fibrin clot that
prevents blood loss and allows the wound to heal.
Plasma and Serum
The liquid component of blood is called plasma, and it can separated from
the blood cells by spinning or centrifuging the blood at high rotations (3000
rpm or higher). The blood cells and platelets are separated by centrifugal
forces to the bottom of a specimen tube. The upper liquid layer, the plasma,
consists of 90 percent water along with various substances required for
maintaining the body’s pH, osmotic load, and for protecting the body. The
plasma also contains the coagulation factors and antibodies.
The plasma component of blood without the coagulation factors is called
the serum. Serum is similar to interstitial fluid in which the correct
composition of key ions acting as electrolytes is essential for normal
functioning of muscles and nerves. Other components in the serum include
proteins that assist with maintaining pH and osmotic balance while giving
viscosity to the blood. The serum also contains antibodies, specialized
proteins that are important for defense against viruses and bacteria. Lipids,
including cholesterol, are also transported in the serum, along with various
other substances including nutrients, hormones, metabolic waste, plus
external substances, such as, drugs, viruses, and bacteria.
Note:
Evolution Connection
Blood Types Related to Proteins on the Surface of the Red Blood Cells
Red blood cells are coated in antigens made of glycolipids and
glycoproteins. The composition of these molecules is determined by
genetics, which have evolved over time. In humans, the different surface
antigens are grouped into 24 different blood groups with more than 100
different antigens on each red blood cell. The two most well known blood
groups are the ABO, shown in [link], and Rh systems. The surface antigens
in the ABO blood group are glycolipids, called antigen A and antigen B.
People with blood type A have antigen A, those with blood type B have
antigen B, those with blood type AB have both antigens, and people with
blood type O have neither antigen. Antibodies are found in the blood
plasma can react with the A or B antigens; individuals with type A blood
have antibodies to thye B blood cells. When type A and type B blood are
combined, agglutination (clumping) of the blood occurs because of
antibodies in the plasma that bind with the opposing antigen; this causes
clots that coagulate in the kidney causing kidney failure and death. Type O
blood has neither A or B antigens, and therefore, type O blood can be
given to all blood types. Type O negative blood is the universal donor.
Type AB positive blood is the universal acceptor because it has both A and
B antigen.
@
(0) (A) (B)
Human red blood cells may have either type A or B
glycoproteins on their surface, both glycoproteins
combined (AB), or neither (O). The glycoproteins serve as
antigens and can elicit an immune response in a person who
receives a transfusion containing unfamiliar antigens. Type
O blood, which has no A or B antigens, does not elicit an
immune response when injected into a person of any blood
type. Thus, O is considered the universal donor. Persons
with type AB blood can accept blood from any blood type,
and type AB is considered the universal acceptor.
(AB)
Mammalian Heart and Blood Vessels
The heart is a complex muscle that pumps blood through the three divisions
of the circulatory system: the coronary (vessels that serve the heart),
pulmonary (heart and lungs), and systemic (systems of the body), as shown
in [link]. Coronary circulation is intrinsic to the heart, and takes blood
directly from the main artery (aorta) coming from the heart to provide
oxygen for the hard-working heart muscle. For pulmonary and systemic
circulation, the heart has to pump blood to the lungs or the rest of the body,
respectively. In vertebrates, the lungs are relatively close to the heart in the
thoracic cavity. The shorter distance to pump means that the heart muscle
wall on the right side of the heart is not as thick as the left side which must
have enough pressure to pump blood all the way to your big toe.
Superior
vena cava
Right
atrium
Pulmonary
artery
Left atrium
Pulmonary
circuit
Pulmonary
vein
Ses? Left ventricle
Inferior |
vena cava Systemic circuit
Right
ventricle
The mammalian circulatory
system is divided into three
circuits: the systemic circuit, the
pulmonary circuit, and the
coronary circuit. Blood is pumped
from veins of the systemic circuit
into the right atrium of the heart,
then into the right ventricle. Blood
then enters the pulmonary circuit,
and is oxygenated by the lungs.
From the pulmonary circuit, blood
re-enters the heart through the left
atrium. From the left ventricle,
blood re-enters the systemic
circuit through the aorta and is
distributed to the rest of the body.
The coronary circuit, which
provides blood to the heart, is not
shown.
Structure of the Heart
The heart muscle is asymmetrical as a result of the distance blood must
travel in the pulmonary and systemic circuits. Since the right side of the
heart sends blood to the pulmonary circuit it is smaller than the left side
which must send blood out to the whole body in the systemic circuit, as
shown in [link]. In humans, the heart is about the size of a clenched fist; it
is divided into four chambers: two atria and two ventricles. There is one
atrium and one ventricle on the right side and one atrium and one ventricle
on the left side. The atria are the chambers that receive blood from the
circulation, and the ventricles are the chambers that pump blood into the
circulation. The right atrium receives deoxygenated blood from the
superior vena cava, which drains blood from the jugular vein that comes
from the brain and from the veins that come from the arms, as well as from
the inferior vena cava which drains blood from the veins that come from
the lower organs and the legs. In addition, the right atrium receives blood
from the coronary sinus which drains deoxygenated blood from the heart
itself. This deoxygenated blood then passes to the right ventricle through
the atrioventricular valve or the tricuspid valve. After it is filled, the right
ventricle pumps the blood through the pulmonary arteries, by-passing the
semilunar valve (or pulmonic valve) to the lungs for re-oxygenation. After
blood passes through the pulmonary arteries, the right semilunar valves
close preventing the blood from flowing backwards into the right ventricle.
The left atrium then receives the oxygen-rich blood from the lungs via the
pulmonary veins. This blood passes through the bicuspid valve or mitral
valve (the atrioventricular valve on the left side of the heart) to the left
ventricle where the blood is pumped out through aorta, the major artery of
the body, taking oxygenated blood to the organs and muscles of the body.
Once blood is pumped out of the left ventricle and into the aorta, the aortic
semilunar valve (or aortic valve) closes preventing blood from flowing
backward into the left ventricle. This pattern of pumping is referred to as
double circulation and is found in all mammals.
The heart has its own blood vessels that supply the heart muscle with blood.
The coronary arteries branch from the aorta and surround the outer surface
of the heart like a crown. They diverge into capillaries where the heart
muscle is supplied with oxygen before converging again into the coronary
veins to take the deoxygenated blood back to the right atrium where the
blood will be re-oxygenated through the pulmonary circuit. The heart
muscle will die without a steady supply of blood. Atherosclerosis is the
blockage of an artery by the buildup of fatty plaques. Because of the size
(narrow) of the coronary arteries and their function in serving the heart
itself, atherosclerosis can be deadly in these arteries. The slowdown of
blood flow and subsequent oxygen deprivation that results from
atherosclerosis causes severe pain, known as angina, and complete blockage
of the arteries will cause myocardial infarction: the death of cardiac muscle
tissue, commonly known as a heart attack.
Arteries, Veins, and Capillaries
The blood from the heart is carried through the body by a complex network
of blood vessels ([link]). Arteries take blood away from the heart. The
main artery is the aorta that branches into major arteries that take blood to
different limbs and organs. These major arteries include the carotid artery
that takes blood to the brain, the brachial arteries that take blood to the
arms, and the thoracic artery that takes blood to the thorax and then into the
hepatic, renal, and gastric arteries for the liver, kidney, and stomach,
respectively. The iliac artery takes blood to the lower limbs. The major
arteries diverge into minor arteries, and then smaller vessels called
arterioles, to reach more deeply into the muscles and organs of the body.
Jugular
veins
Carotid
Aorta artery
Superior Pulmonary
vena Cava arteries
Inferior Pulmonary
vena cava veins
Brachial Heart
ay Thoracic
Basilic aorta
ven Hepatic
Gastric artery
vein Gastric
artery
Renal
artery
lliac vein
lliac artery
The major human arteries and
veins are shown. (credit:
modification of work by
Mariana Ruiz Villareal)
Arterioles diverge into capillary beds. Capillary beds contain a large
number (10 to 100) of capillaries that branch among the cells and tissues of
the body. Capillaries are narrow-diameter tubes that can fit red blood cells
through in single file and are the sites for the exchange of nutrients, waste,
and oxygen with tissues at the cellular level. Fluid also crosses into the
interstitial space from the capillaries. The capillaries converge again into
venules that connect to minor veins that finally connect to major veins that
take blood high in carbon dioxide back to the heart. Veins are blood vessels
that bring blood back to the heart. The major veins drain blood from the
same organs and limbs that the major arteries supply. Fluid is also brought
back to the heart via the lymphatic system.
Systems of Gas Exchange
Introduction
" The inspired and expired air may be sometimes very useful, by
condensing and cooling the blood that passeth through the lungs; I hold that
the depuration of the blood in that passage, is not only one of the ordinary,
but one of the principal uses of respiration." Robert Boyle, in New
Experiments ... Touching the Spring of Air, 1660
The primary function of the respiratory system is to deliver oxygen to the
cells of the body’s tissues and remove a waste product, carbon dioxide (the
process which Boyle called "depuration"). The main structures of the
human respiratory system are the nasal cavity, the trachea, and lungs, and
these structures are what brings oxygen into the human body and removes
carbon dioxide from the human body. As you learned previously, the
circulatory system is responsible for moving oxygen from the lungs to the
tissues and for moving carbon dioxide from the tissues and taking it to the
lungs. At the cellular level the oxygen is needed to make ATP from the
energy stored in glucose and other organic molecules; carbon dioxide is a
waste product of harvesting that energy. In other words, the respiratory
system gets the oxygen inside the body, the circulatory system moves the
oxygen around the body getting it to the cells, the cells use the oxygen to
produce energy and in the process produce carbon dioxide as a waste, the
circulatory system removes the carbon dioxide from the cell and delivers it
to the lungs, and the respiratory system removes the carbon dioxide from
the body. In vertebrates, the respiratory and circulatory work very closely
together in order to allow for gas exchange between the inside and outside
of the organism.
All aerobic organisms require oxygen to carry out their metabolic functions.
Over evolutionary time, different organisms have devised different means
of obtaining oxygen from the surrounding atmosphere. The environment in
which the animal lives greatly determines how an animal respires. The
complexity of the respiratory system is correlated with the size of the
organism. As animal size increases, diffusion distances increase and the
ratio of surface area to volume drops. In unicellular organisms, diffusion
across the plasma membrane is sufficient for supplying oxygen to the cell
({link]). Diffusion is a slow, passive transport process. Therefore,
dependence on diffusion as a means of obtaining oxygen and removing
carbon dioxide remains feasible only for small organisms or those with
highly-flattened bodies, such as many flatworms (Platyhelminthes). Larger
organisms had to evolve specialized respiratory tissues, such as gills, lungs,
and respiratory passages accompanied by a complex circulatory systems, to
transport oxygen throughout their entire body.
The cell of the unicellular
algae Ventricaria
ventricosa is one of the
largest known, reaching
one to five centimeters in
diameter. Like all single-
celled organisms, V.
ventricosa exchanges
gases across the plasma
membrane.
Direct Diffusion
For small multicellular organisms, diffusion across the outer membrane is
sufficient to meet their oxygen needs. Gas exchange by direct diffusion
across surface membranes is efficient for organisms less than 1 mm in
diameter. In simple organisms, such as cnidarians and flatworms, every cell
in the body is close to the external environment. Their cells are kept moist
and gases diffuse quickly via direct diffusion. Flatworms are small, literally
flat worms, which ‘breathe’ through diffusion across the outer surface
({link]). The flat shape of these organisms increases the surface area for
diffusion, ensuring that each cell within the body is close to the outer
surface and has access to oxygen. If the flatworm had a cylindrical body,
then the cells in the center would not be able to get oxygen.
This flatworm’s process of
respiration works by
diffusion across the outer
membrane. (credit: Stephen
Childs)
Skin and Gills
Earthworms and amphibians use their skin (integument) as a respiratory
organ. A dense network of capillaries lies just below the skin and facilitates
gas exchange between the external environment and the circulatory system.
The respiratory surface must be kept moist in order for the gases to dissolve
and diffuse across plasma membranes.
Organisms that live in water need to obtain oxygen from the water. Oxygen
dissolves in water but at a lower concentration than in the atmosphere. The
atmosphere has roughly 21 percent oxygen. In water, the oxygen
concentration is much less than that. Fish and many other aquatic organisms
have evolved gills to take up the dissolved oxygen from water ([link]). Gills
are thin tissue filaments that are highly branched and folded. When water
passes over the gills, the dissolved oxygen in water rapidly diffuses across
the gills into the bloodstream. The circulatory system can then carry the
oxygenated blood to the other parts of the body. In animals that contain
coelomic fluid instead of blood, oxygen diffuses across the gill surfaces into
the coelomic fluid. Gills are found in mollusks, annelids, and crustaceans.
This common carp, like many
other aquatic organisms, has gills
that allow it to obtain oxygen from
water. (credit:
"Guitardude012"/Wikimedia
Commons)
The folded surfaces of the gills provide a large surface area to ensure that
the fish gets sufficient oxygen. Diffusion is a process in which material
travels from regions of high concentration to low concentration until
equilibrium is reached. In this case, blood with a low concentration of
oxygen molecules circulates through the gills. The concentration of oxygen
molecules in water is higher than the concentration of oxygen molecules in
gills. As a result, oxygen molecules diffuse from water (high concentration)
to blood (low concentration), as shown in [link]. Similarly, carbon dioxide
molecules in the blood diffuse from the blood (high concentration) to water
(low concentration).
Water flow
Blood Lamella
By vessels
D
Fy)
4
ri [>
As Z
Oxygen-rich
"a
Oxygen-poor
blood
Gill filaments
As water flows over the gills, oxygen is transferred to blood via
the veins. (credit "fish": modification of work by Duane Raver,
NOAA)
Tracheal Systems
Insect respiration is independent of its circulatory system; therefore, the
blood does not play a direct role in oxygen transport. Insects have a highly
specialized type of respiratory system called the tracheal system, which
consists of a network of small tubes that carries oxygen to the entire body.
The tracheal system is the most direct and efficient respiratory system in
active animals.
Insect bodies have openings, called spiracles, along the thorax and
abdomen. These openings connect to the tubular network, allowing oxygen
to pass into the body ([link]) and regulating the diffusion of CO, and water
vapor. Air enters and leaves the tracheal system through the spiracles. Some
insects can ventilate the tracheal system with body movements.
Tracheal system
Insects perform respiration via a tracheal
system.
Mammalian Systems
In mammals, pulmonary ventilation occurs via inhalation (breathing).
During inhalation, air enters the human body through the nasal cavity
located just inside the nose ({link]). As air passes through the nasal cavity,
the air is warmed to body temperature and humidified. The respiratory tract
is coated with mucus to seal the tissues from direct contact with air. Mucus
is high in water. As air crosses these surfaces of the mucous membranes, it
picks up water. These processes help equilibrate the air to the body
conditions, reducing any damage that cold, dry air can cause. Particulate
matter that is floating in the air is removed in the nasal passages via mucus
and cilia. The processes of warming, humidifying, and removing particles
are important protective mechanisms that prevent damage to the trachea and
lungs. Thus, inhalation serves several purposes in addition to bringing
oxygen into the respiratory system.
Primary
bronchus
Nasal
cavity
Secondary
bronchus
Tertiary
bronchus
Pharynx
Larynx
Bronchiole Trachea
Terminal
bronchiole
Pulmonary
vein
Alveolar sac
Air enters the respiratory
system through the nasal
cavity and pharynx, and then
passes through the trachea
and into the bronchi, which
bring air into the lungs.
(credit: modification of work
by NCI)
From the nasal cavity, air passes through the pharynx (throat) and the
larynx (voice box), as it makes its way to the trachea ([link]). The main
function of the trachea is to funnel the inhaled air to the lungs and the
exhaled air back out of the body. The human trachea is a cylinder about 10
to 12 cm long and 2 cm in diameter that sits in front of the esophagus and
extends from the larynx into the chest cavity where it divides into the two
primary bronchi at the midthorax ([link]). The trachea is lined with mucus-
producing goblet cells and ciliated epithelia. The cilia propel foreign
particles trapped in the mucus toward the pharynx. The cartilage provides
strength and support to the trachea to keep the passage open. The smooth
muscle can contract, decreasing the trachea’s diameter, which causes
expired air to rush upwards from the lungs at a great force. The forced
exhalation helps expel mucus when we cough. Smooth muscle can contract
or relax, depending on stimuli from the external environment or the body’s
nervous system.
Lungs: Bronchi and Alveoli
The end of the trachea bifurcates (divides) to the right and left lungs. The
lungs are not identical. The right lung is larger and contains three lobes,
whereas the smaller left lung contains two lobes ({link]). The muscular
diaphragm, which facilitates breathing, is inferior (below) to the lungs and
marks the end of the thoracic cavity.
Trachea
Left lung
Right lung Upper lobe
Upper lobe
; Lower lobe
Middle lobe
Lower lobe
Diaphragm
The trachea bifurcates into the
right and left bronchi in the lungs.
The right lung is made of three
lobes and is larger. To
accommodate the heart, the left
lung is smaller and has only two
lobes.
In the lungs, air is diverted into smaller and smaller passages, or bronchi.
Air enters the lungs through the two primary (main) bronchi (singular:
bronchus). Each bronchus divides into secondary bronchi, then into tertiary
bronchi, which in turn divide, creating smaller and smaller diameter
bronchioles as they split and spread through the lung.
The terminal bronchioles subdivide into microscopic branches called
respiratory bronchioles. The respiratory bronchioles subdivide into several
alveolar ducts. Numerous alveoli and alveolar sacs surround the alveolar
ducts. The alveolar sacs resemble bunches of grapes tethered to the end of
the bronchioles ({link]). Alveoli are made of thin-walled parenchymal cells,
typically one-cell thick, that look like tiny bubbles within the sacs. Alveoli
are in direct contact with capillaries (one-cell thick) of the circulatory
system. Such intimate contact ensures that oxygen will diffuse from alveoli
into the blood and be distributed to the cells of the body. In addition, the
carbon dioxide that was produced by cells as a waste product will diffuse
from the blood into alveoli to be exhaled.
Alveolar sac Capillaries
Alveolar duct
Mucous gland
Respiratory bronchiole Pulmonary vein
Pulmonary artery Atrium Alveolus
Terminal bronchioles are connected by respiratory bronchioles to
alveolar ducts and alveolar sacs. Each alveolar sac contains 20 to
30 spherical alveoli and has the appearance of a bunch of grapes.
Air flows into the atrium of the alveolar sac, then circulates into
alveoli where gas exchange occurs with the capillaries. Mucous
glands secrete mucous into the airways, keeping them moist and
flexible. (credit: modification of work by Mariana Ruiz Villareal)
Transport of Gases in Blood
Once the oxygen diffuses across the alveoli, it enters the bloodstream and is
transported to the tissues where it is unloaded, and carbon dioxide diffuses
out of the blood and into the alveoli to be expelled from the body. Although
gas exchange is a continuous process, the oxygen and carbon dioxide are
transported by different mechanisms.
Transport of Oxygen in the Blood
Although oxygen dissolves in blood, only a small amount of oxygen is
transported this way. Only 1.5 percent of oxygen in the blood is dissolved
directly into the blood itself. Most oxygen—98.5 percent—is bound to a
protein called hemoglobin and carried to the tissues.
Hemoglobin
Hemoglobin, or Hb, is a protein molecule found in red blood cells
(erythrocytes) made of four subunits: two alpha subunits and two beta
subunits ({link]). Each subunit surrounds a central heme group that
contains iron and binds one oxygen molecule, allowing each hemoglobin
molecule to bind four oxygen molecules. Molecules with more oxygen
bound to the heme groups are brighter red. As a result, oxygenated arterial
blood where the Hb is carrying four oxygen molecules is bright red, while
venous blood that is deoxygenated is darker red.
Oxygen
(a) Red blood cells (b) Hemoglobin
The protein inside (a) red blood cells that carries oxygen to
cells and carbon dioxide to the lungs is (b) hemoglobin.
Hemoglobin is made up of four symmetrical subunits and
four heme groups. Iron associated with the heme binds
oxygen. It is the iron in hemoglobin that gives blood its red
color.
Transport of Carbon Dioxide in the Blood
Carbon dioxide molecules are transported in the blood from body tissues to
the lungs by one of three methods: dissolution directly into the blood,
binding to hemoglobin, or carried as a bicarbonate ion. Several properties of
carbon dioxide in the blood affect its transport. First, carbon dioxide is more
soluble in blood than oxygen. About 5 to 7 percent of all carbon dioxide is
dissolved in the plasma. Second, carbon dioxide can bind to plasma proteins
or can enter red blood cells and bind to hemoglobin. This form transports
about 10 percent of the carbon dioxide. When carbon dioxide binds to
hemoglobin, a molecule called carbaminohemoglobin is formed. Binding of
carbon dioxide to hemoglobin is reversible. Therefore, when it reaches the
lungs, the carbon dioxide can freely dissociate from the hemoglobin and be
expelled from the body.
Third, the majority of carbon dioxide molecules (85 percent) are carried as
part of the bicarbonate buffer system. In this system, carbon dioxide
diffuses into the red blood cells. Carbonic anhydrase (CA) within the red
blood cells quickly converts the carbon dioxide into carbonic acid (H»COs3).
Carbonic acid is an unstable intermediate molecule that immediately
dissociates into bicarbonate ions (HCO, ) and hydrogen (H") ions. Since
carbon dioxide is quickly converted into bicarbonate ions, this reaction
allows for the continued uptake of carbon dioxide into the blood down its
concentration gradient. It also results in the production of H” ions. If too
much H” is produced, it can alter blood pH. However, hemoglobin binds to
the free H* ions and thus limits shifts in pH. The newly synthesized
bicarbonate ion is transported out of the red blood cell into the plasma of
the blood in exchange for a chloride ion (Cl); this is called the chloride
shift. When the blood reaches the lungs, the bicarbonate ion is transported
back into the red blood cell in exchange for the chloride ion. The H” ion
dissociates from the hemoglobin and binds to the bicarbonate ion. This
produces the carbonic acid intermediate, which is converted back into
carbon dioxide through the enzymatic action of CA. The carbon dioxide
produced is expelled through the lungs during exhalation.
Equation:
H2CO3 HCO; + H*
H
CO.+H20 © (carbonic acid) (bicarbonate)
The benefit of the bicarbonate buffer system is that carbon dioxide is
“soaked up” into the blood with little change to the pH of the system. This
is important because it takes only a small change in the overall pH of the
body for severe injury or death to result. The presence of this bicarbonate
buffer system also allows for people to travel and live at high altitudes:
When the partial pressure of oxygen and carbon dioxide change at high
altitudes, the bicarbonate buffer system adjusts to regulate carbon dioxide
while maintaining the correct pH in the body.
Nervous System
Introduction
"We can trace the development of a nervous system, and correlate with it
the parallel phenomena of sensation and thought. We see with undoubting
certainty that they go hand-in-hand. But we try to soar in a vacuum the
moment we seek to comprehend the connexion between them... Man the
object is separated by an impassable gulf from man the subject." John
Tyndall, British physicist, in Fragments of Science for Unscientific People:
A Series of Detached Essays, Lectures and Reviews, 1892
The distinction between the brain and the mind, as described by Tyndall, is
but one of many questions that have fascinated scientists regarding the
human nervous system. Several Nobel Prizes have been awarded to
scientists who have helped elucidate the workings of nerves and nervous
systems, usually with the aid of studies in non-human organisms.
While you’re reading this, your nervous system is performing several
functions simultaneously. The visual system is processing what is seen on
the page; the motor system controls the turn of the pages (or click of the
mouse); the prefrontal cortex maintains attention. Even fundamental
functions, like breathing and regulation of body temperature, are controlled
by the nervous system. A nervous system is an organism’s control center: it
processes sensory information from outside (and inside) the body and
controls all behaviors—from eating to sleeping to studying to finding a
mate.
Diversity of Nervous Systems
Nervous systems throughout the animal kingdom vary in structure and
complexity, as illustrated by the variety of animals shown in [link]. Some
organisms, like sea sponges, lack a true nervous system. Others, like
jellyfish, lack a true brain and instead have a system of separate but
connected nerve cells (neurons) called a “nerve net.” Echinoderms such as
sea Stars have nerve cells that are bundled into fibers called nerves.
Flatworms of the phylum Platyhelminthes have both a central nervous
system (CNS), made up of a small “brain” and two nerve cords, and a
peripheral nervous system (PNS) containing a system of nerves that extend
throughout the body. The insect nervous system is more complex but also
fairly decentralized. It contains a brain, ventral nerve cord, and ganglia
(clusters of connected neurons). These ganglia can control movements and
behaviors without input from the brain. Octopi may have the most
complicated of invertebrate nervous systems—they have neurons that are
organized in specialized lobes and eyes that are structurally similar to
vertebrate species.
Eyespot
\
L
Central
ganglia
(brain)
Nerve ring
‘4. Transverse
Radial nerve
nerves
(a) Cnidarian (b) Echinoderm (c) Planarian
(hydra) ‘sea Star} (flatworm)
Central nervous system
Central ganglia
(brain)
Ganglia
Peripheral
ake nervous
19/7 system
Segmental ganglia Nerve
(d) Arthropod (e) Mollusk (f) Vertebrate
(bee) (octopus) (human)
Nervous systems vary in structure and
complexity. In (a) cnidarians, nerve cells
form a decentralized nerve net. In (b)
echinoderms, nerve cells are bundled into
fibers called nerves. In animals exhibiting
bilateral symmetry such as (c) planarians,
neurons cluster into an anterior brain that
processes information. In addition to a brain,
(d) arthropods have clusters of nerve cell
bodies, called peripheral ganglia, located
along the ventral nerve cord. Mollusks such
as squid and (e) octopi, which must hunt to
survive, have complex brains containing
millions of neurons. In (f) vertebrates, the
brain and spinal cord comprise the central
nervous system, while neurons extending
into the rest of the body comprise the
peripheral nervous system. (credit e:
modification of work by Michael Vecchione,
Clyde F.E. Roper, and Michael J. Sweeney,
NOAA; credit f: modification of work by
NIH)
Compared to invertebrates, vertebrate nervous systems are more complex,
centralized, and specialized. While there is great diversity among different
vertebrate nervous systems, they all share a basic structure: a CNS that
contains a brain and spinal cord and a PNS made up of peripheral sensory
and motor nerves. One interesting difference between the nervous systems
of invertebrates and vertebrates is that the nerve cords of many
invertebrates are located ventrally whereas the vertebrate spinal cords are
located dorsally. There is debate among evolutionary biologists as to
whether these different nervous system plans evolved separately or whether
the invertebrate body plan arrangement somehow “flipped” during the
evolution of vertebrates.
Neurons and Glial Cells
The nervous system is made up of neurons, specialized cells that can
receive and transmit chemical or electrical signals, and glia, cells that
provide support functions for the neurons by playing an information
processing role that is complementary to neurons. A neuron can be
compared to an electrical wire—it transmits a signal from one place to
another. Glia can be compared to the workers at the electric company who
make sure wires go to the right places, maintain the wires, and take down
wires that are broken. This analogy might be oversimplified, however;
recent evidence suggests that glial cells also usurp some of the signaling
functions of neurons.
The nervous system of the common laboratory fly, Drosophila
melanogaster, contains around 100,000 neurons, the same number as a
lobster. This number compares to 75 million in the mouse and 300 million
in the octopus. A human brain contains around 86 billion neurons. Despite
these very different numbers, the nervous systems of these animals control
many of the same behaviors—from basic reflexes to more complicated
behaviors like finding food and courting mates. The ability of neurons to
communicate with each other as well as with other types of cells underlies
all of these behaviors.
There is great diversity in the types of neurons and glia that are present in
different parts of the nervous system. There are three major functional types
of neurons (and many different morphological types), and they share
several important cellular components. But neurons are also highly
specialized—different types of neurons have different sizes and shapes that
relate to their functional roles. There are also several types of glial cells
(astroglia, oligodendrocytes, Schwann cells, etc.) each with different
functions.
Neurons
Parts of a Neuron
Like other cells, each neuron has a cell body (or soma) that contains a
nucleus, smooth and rough endoplasmic reticulum, Golgi apparatus,
mitochondria, and other cellular components. Neurons also contain unique
structures, illustrated in [link] for receiving and sending the electrical
signals that make neuronal communication possible. Dendrites are tree-like
structures that extend away from the cell body to receive messages from
other neurons at specialized junctions called synapses. Although some
neurons do not have any dendrites, some types of neurons have multiple
dendrites.
Once a signal is received by the dendrite, it then travels to the cell body.
The cell body contains a specialized structure, the axon hillock, that
integrates signals from multiple synapses and serves as a junction between
the cell body and an axon. An axon is a tube-like structure that propagates
the integrated signal to specialized endings called axon terminals. These
terminals in turn synapse on other neurons, muscle, or target organs.
Chemicals (known as neurotransmitters) released at axon terminals allow
signals to be communicated to these other cells. Neurons usually have one
or two axons, but some neurons, like amacrine cells in the retina, do not
contain any axons. Some axons are covered with myelin (a product of the
glial cells), which acts as an insulator and greatly increases the speed of
conduction. Along the axon there are periodic gaps in the myelin sheath.
These gaps are called nodes of Ranvier and are sites where the signal is
“recharged” as it travels along the axon.
It is important to note that a single neuron does not act alone—neuronal
communication depends on the connections that neurons make with one
another (as well as with other cells, like muscle cells). Dendrites from a
single neuron may receive synaptic contact from many other neurons. For
example, dendrites from a Purkinje cell in the cerebellum are thought to
receive contact from as many as 200,000 other neurons.
Note:
Cell body (soma)
A
4s 4 2 ye
XH
Axon Oligodendrocyte
Cell membrane
Dendrite e—?
Node of Ranvier
Myelin sheath
Synapse
Neurons contain organelles common to many other cells,
such as a nucleus and mitochondria. They also have more
specialized structures, including dendrites and axons.
Types of Neurons
There are different types of neurons, and the functional role of a given
neuron is intimately dependent on its structure. Although there are only
three functional types of neurons [link], an amazing diversity of neuron
shapes and sizes can found in different parts of the nervous system (and
across species).
Neuron Types
receptor endings
A. Sensory
dendrites ~
oN
Us
(S—
y
axon terminals
axon
a. B: Interneuron
pl
dendrites
a
> —
=>
C.Motor | es
neuron
The three general classes of neurons; all have an input zone (recpetor
endings, dendrites and/or the cell body), an axon, a cell body, and an
output zone (axon terminals). A. Sensory neurons have receptor
endings at one end that are sensitive to various stimuli (e.g. heat,
pressure, light, etc.), a relatively long axon, and axon terminals that
form synapses with dendrites at the other end. B. interneurons receive
signals from sensory neurons via their dendrites at one end, have a
relatively short axon, and pass signals to another neuron via axon
terminals at the other end. C. Motor neurons receive signals via
dendrites at one end, have a long axon, and transmit signals to muscles
or glands at the other end. (Image by Eva Horne)
While there are many defined neuron cell shapes, neurons are broadly
divided into three basic types: sensory, interneuron, and motor neuron. In
general, sensory neurons detect information, either from the external
environment or from internal sources. Examples of sensory neurons include
the pain receptors in your skin and the photoreceptors in your retina. When
activated by the signal to which they are attuned, they send information (via
an action potential) to an interneuron. Interneurons both receive signals
from other neurons and transmit signals to other neurons. The majority of
the cells in your brain and spinal cord are interneurons, communicating
only with other neurons. Interneurons can also send a signal to motor
neurons, which control muscles and endocrine glands.
Glia
While glia are often thought of as the supporting cast of the nervous system,
the number of glial cells in the human brain actually outnumbers the
number of neurons by a factor of ten. Neurons would be unable to function
without the vital roles that are fulfilled by these glial cells. Glia guide
developing neurons to their destinations, buffer ions and chemicals that
would otherwise harm neurons, contribute to the formation of cerebrospinal
fluid, and provide myelin sheaths around axons. Scientists have recently
discovered that they also play a role in responding to nerve activity and
modulating communication between nerve cells. When glia do not function
properly, the result can be disastrous—most brain tumors are caused by
mutations in glia.
How Neurons Communicate
All functions performed by the nervous system—from a simple motor
reflex to more advanced functions like making a memory or a decision—
require neurons to communicate with one another. While humans use words
and body language to communicate, neurons use electrical and chemical
signals. Just like a person in a committee, one neuron usually receives and
synthesizes messages from multiple other neurons before “making the
decision” to send the message on to other neurons.
Nerve Impulse Transmission within a Neuron
For the nervous system to function, neurons must be able to send and
receive signals. These signals are possible because each neuron has a
charged cellular membrane (a voltage difference between the inside and the
outside), and the charge of this membrane can change in response to
neurotransmitter molecules released from other neurons and environmental
stimuli. To understand how neurons communicate, one must first
understand the basis of the baseline or ‘resting’ membrane charge.
Neuronal Charged Membranes
The lipid bilayer membrane that surrounds a neuron is impermeable to
charged molecules or ions. To enter or exit the neuron, ions must pass
through special proteins called ion channels that span the membrane. Ion
channels have different configurations: open, closed, and inactive, as
illustrated in [link]. Some ion channels need to be activated in order to open
and allow ions to pass into or out of the cell. These ion channels are
sensitive to the environment and can change their shape accordingly. Ion
channels that change their structure in response to voltage changes are
called voltage-gated ion channels. Voltage-gated ion channels regulate the
relative concentrations of different ions inside and outside the cell. The
difference in total charge between the inside and outside of the cell is called
the membrane potential.
Voltage-gated Na* Channels
Outside cell
CEASE AE 25 AE 25 2 4
|
OQOOOC™
Cytoplasm
Closed At the resting potential, the Open In response to a nerve impulse, Inactivated For a brief period following
channel is closed. the gate opens and Na* enters the cell. activation, the channel does not open
in response to a new signal.
Voltage-gated ion channels open in response to changes in
membrane voltage. After activation, they become inactivated
for a brief period and will no longer open in response to a
signal.
Resting Membrane Potential
A neuron at rest is negatively charged: the inside of a cell is approximately
70 millivolts more negative than the outside (—70 mV, note that this number
varies by neuron type and by species). This voltage is called the resting
membrane potential; it is generated by differences in the concentrations of
ions inside and outside the cell. If the membrane were equally permeable to
all ions, each type of ion would flow across the membrane and the system
would reach equilibrium. Because ions cannot freely cross the membrane,
and because enzymes can pump ions into or out of a cell, there are different
concentrations of several ions inside and outside the cell, as shown in [link].
The difference in the number of positively charged potassium ions (K*)
inside and outside the cell dominates the resting membrane potential
({link]). When the membrane is at rest, K* ions accumulate inside the cell.
The negative resting membrane potential is created and maintained by
increasing the concentration of cations outside the cell (in the extracellular
fluid) relative to inside the cell (in the cytoplasm); with more positive ions
outside than inside, the inside of the cell is negatively charged (-70mV)
compared to the extracellular space. The negative charge within the cell is
created by the plasma membrane being more permeable to potassium ion
movement than sodium ion movement. In neurons, potassium ions are
maintained at high concentrations within the cell while sodium ions are
maintained at high concentrations outside of the cell. The cell possesses
potassium and sodium leakage channels that allow the two cations to
diffuse down their concentration gradient. However, the neurons have far
more potassium leakage channels than sodium leakage channels. Therefore,
potassium diffuses out of the cell at a much faster rate than sodium leaks in.
Because more cations are leaving the cell than are entering, this causes the
interior of the cell to be negatively charged relative to the outside of the
cell. The actions of the sodium potassium pump help to maintain the resting
potential, once established. Recall that sodium potassium pumps brings two
K" ions into the cell while removing three Na* ions per ATP consumed. As
more cations are expelled from the cell than taken in, the inside of the cell
remains negatively charged relative to the extracellular fluid. It should be
noted that chloride ions (CI-) tend to accumulate outside of the cell because
they are repelled by negatively-charged proteins within the cytoplasm.
Ion Concentration Inside and Outside Neurons
Extracellular Intracellular
concentration concentration Ratio
Ion (mM) (mM) outside/inside
Na‘ 145 12 12
K+ 4 155 0.026
Cl" 120 4 30
Organic
anions — 100
(A-)
The resting membrane potential is a result of different concentrations inside
and outside the cell.
(a) Resting potential
Extracellular fluid (@) Na’)
() (a) ©) (i) Nat channel
yes
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Mt : | ;
©00000000008 100000000 00000000— 000000006 00000006
Qs y\ (3)
@~ © @ © = ©
Nat /K* transporter
At the resting potential, all voltage-gated Na* channels and most voltage-gated K* channels are closed. The Na*/K* transporter
pumps K’* ions into the cell and Na* ions out.
(b) Depolarization
Na’ channel
«) Nat /K* transporter (x) (ve) («) «)
In response to a depolarization, some Na* channels open, allowing Na* ions to enter the cell. The membrane starts to depolarize
(the charge across the membrane lessens). If the threshold of excitation is reached, all the Na* channels open.
(c) Hyperpolarization
K* channel
COOCOCCOCCCOO MM M00 CCCCCE/AM M0CCCCCCe' MD MF \e0e0ee8
OOOOOOOOOOOOW OOOO OOOO OOOOH OHO —
() ©... /K* transporter
At the peak action potential, Na* channels close while K* channels open. K* leaves the cell, and the membrane eventually
becomes hyperpolarized.
The (a) resting membrane potential is a result of
different concentrations of Na* and K” ions inside
and outside the cell. A nerve impulse causes Na*
to rapidly enter the cell, resulting in (b)
depolarization. At the peak action potential, K*
channels open and the cell becomes (c)
hyperpolarized.
Action Potential
A neuron can receive input from other neurons and, if this input is strong
enough, send the signal to downstream neurons. Transmission of a signal
between neurons is generally dependent on chemicals we call
neurotransmitters, which move between nerve cells and their targets.
Transmission of a signal within a neuron (from dendrite to axon terminal) is
initiated by a brief reversal of the resting membrane potential called an
action potential. When neurotransmitter molecules bind to receptors
located on a neuron’s dendrites, ion channels open. At excitatory synapses,
this opening allows positive ions to enter the neuron and results in
depolarization of the membrane—a decrease in the difference in voltage
between the inside and outside of the neuron. A stimulus from a sensory
cell or another neuron depolarizes the target neuron to its threshold
potential (-55 mV). Na* channels in the axon hillock open, allowing
positive ions to enter the cell ([link] and [link]). Once the sodium channels
open, the neuron completely depolarizes to a membrane potential of about
+40 mV. Action potentials are considered an "all-or nothing" event, in that,
once the threshold potential is reached, the neuron always completely
depolarizes. Once depolarization is complete, the cell must now "reset" its
membrane voltage back to the resting potential. To accomplish this, the Na*
channels close and cannot be opened. This begins the neuron's refractory
period, in which it cannot produce another action potential because its
sodium channels will not open. At the same time, voltage-gated K*
channels open, allowing K* to leave the cell. As K* ions leave the cell, the
membrane potential once again becomes negative. The diffusion of K* out
of the cell actually hyperpolarizes the cell, in that the membrane potential
becomes more negative than the cell's normal resting potential. At this
point, the sodium channels will return to their resting state, meaning they
are ready to open again if the membrane potential again exceeds the
threshold potential.
Note:
Membrane potential (mV)
+30
Repolarization
Threshold of
excitation
Hyperpolarization
Time
The formation of an action
potential can be divided into
five steps: (1) A stimulus from a
sensory cell or another neuron
causes the target cell to
depolarize toward the threshold
potential. (2) If the threshold of
excitation is reached, all Na*
channels open and the
membrane depolarizes. (3) At
the peak action potential, K*
channels open and K* begins to
leave the cell. At the same time,
Na* channels close. (4) The
membrane becomes
hyperpolarized as K* ions
continue to leave the cell. The
hyperpolarized membrane is in
a refractory period and cannot
fire. (5) The K* channels close
and the Na*/K* transporter
restores the resting potential.
Peak action potential
ee
Direction of travel of action potential
a. In response to a signal, the
soma end of the axon becomes
depolarized.
b. The depolarization spreads down
the axon. Meanwhile, the first part of
the membrane repolarizes. Because
Na* channels are inactivated and
additional K* channels have opened,
the membrane cannot depolarize again.
c. The action potential continues to
travel down the axon.
The action potential is conducted down the axon as the axon
membrane depolarizes, then repolarizes.
Synaptic Transmission
The synapse or “gap” is the place where information is transmitted from
one neuron to another. Synapses usually form between axon terminals and
dendritic spines, but this is not universally true. There are also axon-to-
axon, dendrite-to-dendrite, and axon-to-cell body synapses. The neuron
transmitting the signal is called the presynaptic neuron, and the neuron
receiving the signal is called the postsynaptic neuron. Note that these
designations are relative to a particular synapse—most neurons are both
presynaptic and postsynaptic. There are two types of synapses: chemical
and electrical.
Chemical Synapse
When an action potential reaches the axon terminal it depolarizes the
membrane and opens voltage-gated Na* channels. Na* ions enter the cell,
further depolarizing the presynaptic membrane. This depolarization causes
voltage-gated Ca** channels to open. Calcium ions entering the cell initiate
a signaling cascade that causes small membrane-bound vesicles, called
synaptic vesicles, containing neurotransmitter molecules to fuse with the
presynaptic membrane. Synaptic vesicles are shown in [link], which is an
image from a scanning electron microscope.
This pseudocolored image taken
with a scanning electron
microscope shows an axon
terminal that was broken open to
reveal synaptic vesicles (blue and
orange) inside the neuron. (credit:
modification of work by Tina
Carvalho, NIH-NIGMS; scale-bar
data from Matt Russell)
Fusion of a vesicle with the presynaptic neuronal plasma membrane causes
neurotransmitter to be released into the synaptic cleft, the extracellular
space between the presynaptic and postsynaptic cells, as illustrated in [link].
The neurotransmitter diffuses across the synaptic cleft and binds to receptor
proteins on the postsynaptic cell's plasma membrane.
pS Presynaptic
neuron
©@ Action potential
arrives at axon
terminal.
Axon terminal
Ca?* entry causes
neurotransmitter-containing
synaptic vesicles to release
their contents by exocytosis.
Synaptic
vesicles
Synaptic cleft @ Voltage-gated Ca2*
channels open and
Ca?* enters the
axon terminal.
Neurotransmitter diffuses across
the synaptic cleft and binds to
ligand-gated ion channels on the
postsynaptic membrane.
Localized membrane
potential
lon movement
if
(2 a
SHH SECEHOSESOALOE
Binding of neurotransmitter opens ligand-gated © Reuptake by the presynapic neuron, enzymatic degradation,
ion channels, resulting in graded potentials. and diffusion reduce neurotransmitter levels, terminating the
signal.
Communication at chemical synapses requires release of
neurotransmitters. When the presynaptic membrane is
depolarized, voltage-gated Ca** channels open and allow
Ca?* to enter the cell. The calcium entry causes synaptic
vesicles to fuse with the membrane and release
neurotransmitter molecules into the synaptic cleft. The
neurotransmitter diffuses across the synaptic cleft and
binds to ligand-gated ion channels in the postsynaptic
membrane, resulting in a localized depolarization or
hyperpolarization of the postsynaptic neuron.
The binding of a specific neurotransmitter causes particular ion channels on
the postsynaptic membrane to open. Unlike the sodium channels which
respond to a change in the membrane voltage (i.e., voltage-gated channels),
these ion channels are classified as ligand-gated, since they open the gates
in response to binding of the ligand (neurotransmitter). Neurotransmitters
can either have excitatory or inhibitory effects on the postsynaptic
membrane, as detailed in [link]. For example, when acetylcholine is
released at the synapse between a nerve and muscle (called the
neuromuscular junction) by a presynaptic neuron, it causes postsynaptic
Na* channels to open. Na’ enters the postsynaptic cell and causes the
postsynaptic membrane to depolarize.
Once neurotransmission has occurred, the neurotransmitter must be
removed from the synaptic cleft so the postsynaptic membrane can “reset”
and be ready to receive another signal. This can be accomplished in three
ways: the neurotransmitter can diffuse away from the synaptic cleft, it can
be degraded by enzymes in the synaptic cleft, or it can be recycled
(sometimes called re-uptake) by the presynaptic neuron. Several drugs act
at this step of neurotransmission. For example, cocaine acts to inhibit re-
uptake of neurotransmitters, which acts to prolong the excitatory stimulus
initiated by those neurotransmitters. Many of the well-known antidepressant
drugs work in the same way.
Neurotransmitter Function and Location
Neurotransmitter Example Location
CNS
Acetylcholine — and/or
PNS
CNS
Dopamine, serotonin,
Biogenic amine nGrenasehiine and/or
pinep PNS
Read Glycine, glutamate, aspartate, CNS
gamma aminobutyric acid
CNS
Neuropeptide Substance P, endorphins and/or
PNS
Electrical Synapses
While electrical synapses are fewer in number than chemical synapses, they
are found in all nervous systems and play important and unique roles. The
mode of neurotransmission in electrical synapses is quite different from that
in chemical synapses. In an electrical synapse, the presynaptic and
postsynaptic membranes are very close together and are actually physically
connected by channel proteins forming gap junctions. Gap junctions allow
current to pass directly from one cell to the next. In addition to the ions that
carry this current, other molecules (e.g. ATP, or signaling ions like Ca**),
can diffuse through the large gap junction pores.
There are key differences between chemical and electrical synapses.
Because chemical synapses depend on the release of neurotransmitter
molecules from synaptic vesicles to pass on their signal, there is an
approximately one millisecond delay between when the axon potential
reaches the presynaptic terminal and when the neurotransmitter leads to
opening of postsynaptic ion channels. Additionally, this signaling is
unidirectional. Signaling in electrical synapses, in contrast, is virtually
instantaneous (which is important for synapses involved in key reflexes),
and some electrical synapses are bidirectional. Electrical synapses are also
more reliable as they are less likely to be blocked, and they are important
for synchronizing the electrical activity of a group of neurons. For example,
electrical synapses in the thalamus are thought to regulate slow-wave sleep,
and disruption of these synapses can cause seizures.
Central Nervous System
The central nervous system (CNS) is made up of the brain, a part of which
is shown in [link] and spinal cord and is covered with three layers of
protective coverings called meninges (from the Greek word for membrane).
The outermost layer is the dura mater (Latin for “hard mother”). As the
Latin suggests, the primary function for this thick layer is to protect the
brain and spinal cord. The dura mater also contains vein-like structures that
carry blood from the brain back to the heart. The middle layer is the web-
like arachnoid mater. The last layer is the pia mater (Latin for “soft
mother”), which directly contacts and covers the brain and spinal cord like
plastic wrap. The space between the arachnoid and pia maters is filled with
cerebrospinal fluid (CSF). CSF is produced by a tissue called choroid
plexus in fluid-filled compartments in the CNS called ventricles. The brain
floats in CSF, which acts as a cushion and shock absorber and makes the
brain neutrally buoyant. CSF also functions to circulate chemical
substances throughout the brain and into the spinal cord.
The entire brain contains only about 8.5 tablespoons of CSF, but CSF is
constantly produced in the ventricles. This creates a problem when a
ventricle is blocked—the CSF builds up and creates swelling and the brain
is pushed against the skull. This swelling condition is called hydrocephalus
(“water head”) and can cause seizures, cognitive problems, and even death
if a shunt is not inserted to remove the fluid and pressure.
Skin Veins
Dura mater Arachnoid
mater
Pia mater Cerebral
cortex
The cerebral cortex is covered by
three layers of meninges: the dura,
arachnoid, and pia maters. (credit:
modification of work by Gray’s
Anatomy)
Brain
The brain is the part of the central nervous system that is contained in the
cranial cavity of the skull. It includes the cerebral cortex, limbic system,
basal ganglia, thalamus, hypothalamus, and cerebellum. There are three
different ways that a brain can be sectioned in order to view internal
structures: a Sagittal section cuts the brain left to right, as shown in [link]b,
a coronal section cuts the brain front to back, as shown in [link]a, and a
horizontal section cuts the brain top to bottom.
Cerebral Cortex
The outermost part of the brain is a thick piece of nervous system tissue
called the cerebral cortex, which is folded into hills called gyri (singular:
gyrus) and valleys called sulci (singular: sulcus). The cortex is made up of
two hemispheres—right and left—which are separated by a large sulcus. A
thick fiber bundle called the corpus callosum (Latin: “tough body”)
connects the two hemispheres and allows information to be passed from one
side to the other. Although there are some brain functions that are localized
more to one hemisphere than the other, the functions of the two
hemispheres are largely redundant. In fact, sometimes (very rarely) an
entire hemisphere is removed to treat severe epilepsy. While patients do
suffer some deficits following the surgery, they can have surprisingly few
problems, especially when the surgery is performed on children who have
very immature nervous systems.
Corpus callosum
Basal { >
ganglia "
Gyri \
Right
hemisphere
of the
cerebral
cortex
Thalamus
Amygdala Cerebellum
Cerebellum Brainstem
(a) Coronal section (b) Sagittal section
Brainstem
These illustrations show the (a) coronal and (b) sagittal
sections of the human brain.
Each cortical hemisphere contains regions called lobes that are involved in
different functions. Scientists use various techniques to determine what
brain areas are involved in different functions: they examine patients who
have had injuries or diseases that affect specific areas and see how those
areas are related to functional deficits. They also conduct animal studies
where they stimulate brain areas and see if there are any behavioral
changes. They use a technique called transmagnetic stimulation (TMS) to
temporarily deactivate specific parts of the cortex using strong magnets
placed outside the head; and they use functional magnetic resonance
imaging (fMRI) to look at changes in oxygenated blood flow in particular
brain regions that correlate with specific behavioral tasks. These techniques,
and others, have given great insight into the functions of different brain
regions but have also showed that any given brain area can be involved in
more than one behavior or process, and any given behavior or process
generally involves neurons in multiple brain areas. That being said, each
hemisphere of the mammalian cerebral cortex can be broken down into four
functionally and spatially defined lobes: frontal, parietal, temporal, and
occipital. [link] illustrates these four lobes of the human cerebral cortex.
Motor cortex
Somatosensory
cortex
Frontal lobe
Parietal lobe
Olfactory bulb
Temporal lobe
Cerebellum
Spinal cord
The human cerebral cortex
includes the frontal, parietal,
temporal, and occipital lobes.
The frontal lobe is located at the front of the brain, over the eyes. This lobe
contains the olfactory bulb, which processes odors. The frontal lobe also
contains the motor cortex, which is important for planning and
implementing movement. Areas within the motor cortex map to different
muscle groups, and there is some organization to this map, as shown in
[link]. For example, the neurons that control movement of the fingers are
next to the neurons that control movement of the hand. Neurons in the
frontal lobe also control cognitive functions like maintaining attention,
speech, and decision-making. Studies of humans who have damaged their
frontal lobes show that parts of this area are involved in personality,
socialization, and assessing risk.
Wrists .
Elbows Fingers
Shoulders
Thumbs
Eyebrows
and eyelids
Eyeballs
Face
Cerebral
cortex ma
Jaw
Tongue
Motor cortex
(right hemisphere)
Salivation
Chewing
Swallowing
Different parts of the motor
cortex control different muscle
groups. Muscle groups that are
neighbors in the body are
generally controlled by
neighboring regions of the
motor cortex as well. For
example, the neurons that
control finger movement are
near the neurons that control
hand movement.
The parietal lobe is located at the top of the brain. Neurons in the parietal
lobe are involved in speech and also reading. Two of the parietal lobe’s
main functions are processing somatosensation—touch sensations like
pressure, pain, heat, cold—and processing proprioception—the sense of
how parts of the body are oriented in space. The parietal lobe contains a
somatosensory map of the body similar to the motor cortex.
The occipital lobe is located at the back of the brain. It is primarily involved
in vision—seeing, recognizing, and identifying the visual world.
The temporal lobe is located at the base of the brain by your ears and is
primarily involved in processing and interpreting sounds. It also contains
the hippocampus (Greek for “seahorse”)—a structure that processes
memory formation. The hippocampus is illustrated in [link]. The role of the
hippocampus in memory was partially determined by studying one famous
epileptic patient, HM, who had both sides of his hippocampus removed in
an attempt to cure his epilepsy. His seizures went away, but he could no
longer form new memories (although he could remember some facts from
before his surgery and could learn new motor tasks).
Hypothalamus
One small but critically important part of the brain is the hypothalamus,
shown in [link]. The hypothalamus controls the endocrine system by
sending signals to the pituitary gland, a pea-sized endocrine gland that
releases several different hormones that affect other glands as well as other
cells. This relationship means that the hypothalamus regulates many
important behaviors that are controlled by these hormones. The
hypothalamus is the body’s thermostat—it makes sure key functions like
food and water intake, energy expenditure, and body temperature are kept at
appropriate levels. Neurons within the hypothalamus also regulate circadian
rhythms, sometimes called sleep cycles.
Cerebellum
The cerebellum (Latin for “little brain”), shown in [link], sits at the base of
the brain on top of the brainstem. The cerebellum controls balance and aids
in coordinating movement and learning new motor tasks.
Brainstem
The brainstem, illustrated in [link], connects the rest of the brain with the
spinal cord. It consists of the midbrain, medulla oblongata, and the pons.
Motor and sensory neurons extend through the brainstem allowing for the
relay of signals between the brain and spinal cord. Ascending neural
pathways cross in this section of the brain allowing the left hemisphere of
the cerebrum to control the right side of the body and vice versa. The
brainstem coordinates motor control signals sent from the brain to the body.
The brainstem controls several important functions of the body including
alertness, arousal, breathing, blood pressure, digestion, heart rate,
swallowing, walking, and sensory and motor information integration.
Spinal Cord
Connecting to the brainstem and extending down the body through the
spinal column is the spinal cord, shown in [link]. The spinal cord is a thick
bundle of nerve tissue that carries information about the body to the brain
and from the brain to the body. The spinal cord is contained within the
bones of the vertebrate column but is able to communicate signals to and
from the body through its connections with spinal nerves (part of the
peripheral nervous system). A cross-section of the spinal cord looks like a
white oval containing a gray butterfly-shape, as illustrated in [link].
Myelinated axons make up the “white matter” and neuron and glial cell
bodies make up the “gray matter.” Gray matter is also composed of
interneurons, which connect two neurons each located in different parts of
the body. Axons and cell bodies in the dorsal (facing the back of the animal)
spinal cord convey mostly sensory information from the body to the brain.
Axons and cell bodies in the ventral (facing the front of the animal) spinal
cord primarily transmit signals controlling movement from the brain to the
body.
The spinal cord also controls motor reflexes. These reflexes are quick,
unconscious movements—like automatically removing a hand from a hot
object. Reflexes are so fast because they involve local synaptic connections.
For example, the knee reflex that a doctor tests during a routine physical is
controlled by a single synapse between a sensory neuron and a motor
neuron. While a reflex may only require the involvement of one or two
synapses, synapses with interneurons in the spinal column transmit
information to the brain to convey what happened (the knee jerked, or the
hand was hot).
In the United States, there around 10,000 spinal cord injuries each year.
Because the spinal cord is the information superhighway connecting the
brain with the body, damage to the spinal cord can lead to paralysis. The
extent of the paralysis depends on the location of the injury along the spinal
cord and whether the spinal cord was completely severed. For example, if
the spinal cord is damaged at the level of the neck, it can cause paralysis
from the neck down, whereas damage to the spinal column further down
may limit paralysis to the legs. Spinal cord injuries are notoriously difficult
to treat because spinal nerves do not regenerate, although ongoing research
suggests that stem cell transplants may be able to act as a bridge to
reconnect severed nerves. Researchers are also looking at ways to prevent
the inflammation that worsens nerve damage after injury. One such
treatment is to pump the body with cold saline to induce hypothermia. This
cooling can prevent swelling and other processes that are thought to worsen
spinal cord injuries.
White matter Gray matter
=~ Dorsal horn
Ventral horn
A cross-section of the spinal
cord shows gray matter
(containing cell bodies and
interneurons) and white matter
(containing axons).
Peripheral Nervous System
The peripheral nervous system (PNS) is the connection between the central
nervous system and the rest of the body. The CNS is like the power plant of
the nervous system. It creates the signals that control the functions of the
body. The PNS is like the wires that go to individual houses. Without those
“wires,” the signals produced by the CNS could not control the body (and
the CNS would not be able to receive sensory information from the body
either).
The PNS consists of the sensory division (afferent), which consists of
sensory neurons, and the motor division (efferent), which consists of motor
neurons. The sensory division conveys information to the CNS to be
processed, and the motor division conveys the response of the CNS to
muscles, glands and organs. The motor component of the PNS is even more
complex and can be divided into the autonomic division and the somatic
division. The autonomic motor division, as the name implies, is not
controlled or initiated by the conscious thought of an individual. The
somatic motor division is consciously controlled by the individual and
usually affects skeletal muscles.
Autonomic Motor Division
Note:
Autonomic Motor Division
Preganglionic
neuron: soma is /
usually in the brain- [
stem or sacral
(toward the bottom)
spinal cord
ganglion near the
target organ
Neurotransmitters
released from
postganglionic
synapse: oF
acetylcholine or nitric |
oxide
response is activated response is activated
In the autonomic motor division of the
peripheral nervous system, a preganglionic
neuron of the CNS synapses with a
postganglionic neuron of the PNS. The
postganglionic neuron, in turn, acts on a target
organ. Autonomic responses are mediated by
the sympathetic and the parasympathetic
systems, which are antagonistic to one another.
The sympathetic system activates the “fight or
flight” response, while the parasympathetic
system activates the “rest and digest” response.
The autonomic motor division serves as the relay between the CNS and the
internal organs. It controls the lungs, the heart, smooth muscle, and
exocrine and endocrine glands. The autonomic motor division controls
these organs largely without conscious control; it can continuously monitor
the conditions of these different systems and implement changes as needed.
Signaling to the target tissue usually involves two synapses: a preganglionic
neuron (originating in the CNS) synapses to a neuron in a ganglion that, in
turn, synapses on the target organ, as illustrated in [link]. There are two
divisions of the autonomic motor division that often have opposing effects:
the sympathetic division and the parasympathetic division.
Sympathetic Division
The sympathetic division is responsible for the “fight or flight” response
that occurs when an animal encounters a dangerous situation. One way to
remember this is to think of the surprise a person feels when encountering a
snake (“snake” and “sympathetic” both begin with “s”). Examples of
functions controlled by the sympathetic division include an accelerated
heart rate and inhibited digestion. These functions help prepare an
organism’s body for the physical strain required to escape a potentially
dangerous situation or to fend off a predator.
Parasympathetic Nervous System Sympathetic Nervous System
oS
(NS
Constricts pupil Dilates pupil
Stimulates salivation Inhibits salivation
Slows heart rate Increases heart rate
Dilates bronchi
Constricts bronchi
Solar plexus Inhibits digestion
Stimulates digestion
Stimulates the breakdown
of glycogen
Stimulates bile secretion
Stimulates secretion of
adrenaline and noradrenaline
Causes bladder to contract
Inhibits contraction of bladder
Sacral
The sympathetic and parasympathetic divisions often have
opposing effects on target organs.
Most preganglionic neurons in the sympathetic division originate in the
spinal cord, as illustrated in [link]. The axons of these neurons release
acetylcholine on postganglionic neurons within sympathetic ganglia (the
sympathetic ganglia form a chain that extends alongside the spinal cord).
The acetylcholine activates the postganglionic neurons. Postganglionic
neurons then release norepinephrine onto target organs. As anyone who
has ever felt a rush before a big test, speech, or athletic event can attest, the
effects of the sympathetic division are quite pervasive. This is both because
one preganglionic neuron synapses on multiple postganglionic neurons,
amplifying the effect of the original synapse, and because the adrenal gland
also releases norepinephrine (and the closely related hormone epinephrine)
into the blood stream. The physiological effects of this norepinephrine
release include dilating the trachea and bronchi (making it easier for the
animal to breathe), increasing heart rate, and moving blood from the skin to
the heart, muscles, and brain (so the animal can think and run). The strength
and speed of the sympathetic response helps an organism avoid danger.
Parasympathetic Division
While the sympathetic division is activated in stressful situations, the
parasympathetic division allows an animal to “rest and digest.” One way
to remember this is to think that during a restful situation like a picnic, the
parasympathetic division is in control (“picnic” and “parasympathetic” both
start with “p”). Parasympathetic preganglionic neurons have cell bodies
located in the brainstem and in the sacral (toward the bottom) spinal cord,
as shown in [link]. The axons of the preganglionic neurons release
acetylcholine on the postganglionic neurons, which are generally located
very near the target organs. Most postganglionic neurons release
acetylcholine onto target organs, although some release nitric oxide.
The parasympathetic division resets organ function after the sympathetic
division is activated (the common adrenaline dump you feel after a ‘fight-
or-flight’ event). Effects of acetylcholine release on target organs include
slowing of heart rate, lowered blood pressure, and stimulation of digestion.
Somatic Division
The somatic division of the peripheral nervous system is made up of cranial
and spinal nerves the contain motor neurons. Motor neurons transmit
messages about desired movement from the CNS to the muscles to make
them contract. Without its somatic division, an animal would be unable to
process any information about its environment (what it sees, feels, hears,
and so on) and could not control motor movements. Unlike the autonomic
division, which has two synapses between the CNS and the target organ,
motor neurons of the somatic division have only one synapse between the
CNS and muscle or organ. Acetylcholine is the main neurotransmitter
released at these synapses.
Cranial and Spinal Nerves
Humans have 12 cranial nerves, nerves that emerge from or enter the skull
(cranium), as opposed to the spinal nerves, which emerge from the vertebral
column. Each cranial nerve is accorded a name, which are detailed in [link].
Some cranial nerves transmit only sensory information. For example, the
olfactory nerve transmits information about smells from the nose to the
brainstem. Other cranial nerves transmit almost solely motor information.
For example, the oculomotor nerve controls the opening and closing of the
eyelid and some eye movements. Other cranial nerves contain a mix of
sensory and motor fibers. For example, the glossopharyngeal nerve has a
role in both taste (sensory) and swallowing (motor).
Olfactory
Optic
Oculomotor
Trochlear
Trigeminal
Abducens ‘
Facial
Vestibulocochlear
Glossopharyngeal
Hypoglossal
Vagus
_. il —— wy
The human brain contains 12 cranial nerves that receive
sensory input and control motor output for the head and neck.
Spinal nerves transmit sensory and motor information between the spinal
cord and the rest of the body. Each of the 31 spinal nerves (in humans)
contains both sensory and motor axons. The sensory neuron cell bodies are
grouped in structures called dorsal root ganglia and are shown in [link].
Each sensory neuron has one projection—with a sensory receptor ending in
skin, muscle, or sensory organs—and another that synapses with a neuron
in the dorsal spinal cord. Motor neurons have cell bodies in the ventral gray
matter of the spinal cord that project to muscle through the ventral root.
These neurons are usually stimulated by interneurons within the spinal cord
but are sometimes directly stimulated by sensory neurons.
Dorsal root
White matter e
anglion
Dorsal root
Gray matter Seay
neuron
soma
Motor neuron Ventral root
soma
Cross Section of Spinal Cord
Spinal nerves contain both
sensory and motor axons. The
somas of sensory neurons are
located in dorsal root ganglia.
The somas of motor neurons are
found in the ventral portion of
the gray matter of the spinal
cord.
Endocrine System
"The specific character of the greater part of the toxins which are known to
us (I need only instance such toxins as those of tetanus and diphtheria)
would suggest that the substances produced for effecting the corrleation of
organs within the body, through the intermediation of the blood stream,
might also belong to this class, since here also specificity of action must be
a distinguishing characteristic. These chemical messengers, however, or
"hormones"(from the Greek OppQv, to excite or arouse), as we might call
them, have to be carried from the organ where they are produced to the
organ which they affect by means of the blood stream, and the continually
recurring physiological needs of the organism must determine their repeated
production and circulation throughout the body. " Ernest Henry Starling,
"The Chemical Correlation of the Functions of the Body", The Lancet,
1905, II, 340
Hormones, as Starling noted, are produced by one organ and affect the
activities of other organs. Unlike neurotransmitters, which you will learn
about later in this module, hormones move via the bloodstream from the
site of production to the site of action. But like neurotransmitters, hormones
are key players in maintaining homeostasis. Before we discuss that,
however, we need to review homeostasis and introduce the major classes of
animal hormones.
Types of Hormones
Maintaining homeostasis within the body requires the coordination of many
different systems and organs. Communication between neighboring cells,
and between cells and tissues in distant parts of the body, occurs through
the release of chemicals called hormones. Hormones are chemicals that are
released by cells into body fluids (usually blood) and which act on target
cells at some distance from the cells that release the hormone. At the target
cells, which are cells that have a receptor for the chemical, the hormones
elicit a response. The cells, tissues, and organs that secrete hormones make
up the endocrine system. Examples of glands of the endocrine system
include the adrenal glands, which produce hormones such as epinephrine
and norepinephrine that regulate responses to stress, and the thyroid gland,
which produces thyroid hormones that regulate metabolic rates.
Although there are many different hormones in the human body, they can
be divided into two general classes based on their chemical structure and
water solubility: steroid hormones (most are derivatives of cholesterol),
which are not soluble in water, and peptide (peptides and proteins)
hormones, which are readily soluble in water. One of the key distinguishing
features of lipid-derived hormones is that they can diffuse across plasma
membranes whereas the peptide hormones cannot.
Lipid-Derived Hormones (or Lipid-soluble Hormones)
Most lipid hormones are derived from cholesterol and thus are structurally
similar to it, as illustrated in [link]. The primary class of lipid hormones in
humans is the steroid hormones. Examples of steroid hormones include
estradiol, which is an estrogen, or female sex hormone, and testosterone,
which is an androgen, or male sex hormone. These two hormones are
released by the female and male reproductive organs, respectively. Other
steroid hormones include aldosterone and cortisol, which are released by
the adrenal glands along with some other types of androgens. Steroid
hormones are insoluble in water, and need to be bound to transport proteins
in order to be transported in the blood. As a result, they remain in the body
longer than peptide hormones. For example, cortisol has a half-life of 60 to
90 minutes in humans, while epinephrine, an amino acid derived-hormone,
has a half-life of approximately one minute.
CH3 OH
CH,
(a) Cholesterol (b) Testosterone
HO
(c) Estradiol
The structures shown here represent (a)
cholesterol, plus the steroid hormones (b)
testosterone and (c) estradiol.
Peptide (water-soluble) Hormones
The peptide hormones include polypeptides as well as several relatively
small molecules that are derived from the amino acids tyrosine and
tryptophan, shown in [link]. Examples of amino acid-derived hormones
include epinephrine and norepinephrine, which are synthesized in the
medulla of the adrenal glands, and thyroxine, which is produced by the
thyroid gland. The pineal gland in the brain makes and secretes melatonin
which regulates sleep cycles.
oO OH H
Ho ‘
OH cu,
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Tyrosine Epinephrine
(a)
i |
HN.
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Tryptophan Melatonin
(b)
(a) The hormone epinephrine, which triggers
the fight-or-flight response, is derived from the
amino acid tyrosine. (b) The hormone
melatonin, which regulates circadian rhythms,
is derived from the amino acid tryptophan.
Other peptide hormones are polypeptides (chains of amino acids linked by
peptide bonds). These hormones include molecules that are quite short
polypeptide chains, such as antidiuretic hormone (9 amino acids) and
oxytocin (also 9 amino acids), both of which are produced in the brain and
released into the blood in the posterior pituitary gland. This class also
includes small proteins, like the growth hormones (approx 190 amino acids(
produced by the pituitary, and large glycoproteins such as follicle-
stimulating hormone (a complex of 2 different polypeptides, each about 100
amino acids in length), produced by the pituitary. [link] illustrates these
peptide hormones.
Secreted peptides like insulin are stored within vesicles in the cells that
synthesize them. They are then released in response to stimuli such as high
blood glucose levels in the case of insulin. Amino acid-derived and
polypeptide hormones are water-soluble. Therefore these hormones cannot
cross the plasma membranes of cells; their receptors are found on the
surface of the target cells.
(a) (c)
The structures of peptide hormones (a) oxytocin, (b)
growth hormone, and (c) follicle-stimulating hormone
are shown. These peptide hormones are much larger
than those derived from cholesterol or amino acids.
How Hormones Work
Hormones mediate changes in target cells after binding to specific hormone
receptors. In this way, even though hormones circulate throughout the body
and come into contact with many different cell types, they only affect cells
that possess the necessary receptors. Receptors for a specific hormone may
be found on many different cells or may be limited to a small number of
specialized cells. For example, thyroid hormones act on many different
tissue types, stimulating metabolic activity throughout the body;
testosterone receptors are found in relatively few cell types. Cells can have
many receptors for the same hormone but often also possess receptors for
different types of hormones. The number of receptors that respond to a
hormone determines the cell’s sensitivity to that hormone, and the resulting
cellular response.
Receptor binding alters cellular activity and results in an increase or
decrease in normal body processes. Depending on the location of the
protein receptor on the target cell and the chemical structure of the
hormone, hormones can mediate changes directly by binding to
intracellular hormone receptors and modulating gene transcription, or
indirectly by binding to cell surface receptors and stimulating signaling
pathways.
Intracellular Hormone Receptors
Lipid-soluble hormones such as steroid hormones diffuse across the
membranes of the cells where they are produced. Once outside the cell, they
bind to transport proteins that keep them soluble in the bloodstream. At the
target cell, the hormones are released from the carrier protein and diffuse
across the lipid bilayer of the plasma membrane of cells. The steroid
hormones pass through the plasma membrane of a target cell and bind to
intracellular receptors residing in the cytoplasm or in the nucleus. The cell
signaling pathways induced by the steroid hormones regulate specific genes
on the cell's DNA. The hormones and receptor complex act as transcription
regulators by increasing or decreasing the synthesis of mRNA molecules of
specific genes. The cellular responses are varied, ranging from changes in
the structure of the cell to the production of enzymes that catalyze new
chemical reactions. In this way, the steroid hormone regulates specific cell
processes as illustrated in [link].
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An intracellular nuclear receptor (NR) is located in the
cytoplasm bound to a heat shock protein (HSP). Upon
hormone binding, the receptor dissociates from the heat
shock protein and translocates to the nucleus. In the nucleus,
the hormone-receptor complex binds to a DNA sequence
called a hormone response element (HRE), which triggers
gene transcription and translation. The corresponding
protein product can then mediate changes in cell function.
Other lipid-soluble hormones that are not steroid hormones, such as vitamin
D and thyroxine, have receptors located in the nucleus. The hormones
diffuse across both the plasma membrane and the nuclear envelope, then
bind to receptors in the nucleus. The hormone-receptor complex stimulates
transcription of specific genes.
Plasma Membrane Hormone Receptors
Peptide hormones are not lipid-soluble, and therefore cannot diffuse
through the plasma membrane of cells. Lipid insoluble hormones bind to
receptors on the outer surface of the plasma membrane. Unlike steroid
hormones, lipid insoluble hormones do not directly affect the target cell
because they cannot enter the cell and act directly on DNA. Binding of
these hormones to a cell surface receptor results in activation of a signaling
pathway; this triggers intracellular activity and carries out the specific
effects associated with the hormone. In this way, nothing passes through the
plasma membrane; the hormone that binds at the surface remains at the
surface of the cell while the intracellular product remains inside the cell.
The hormone that initiates the signaling pathway is called a first messenger,
which activates a second messenger in the cytoplasm, as illustrated in
[link].
B-Adrenergic receptor Epinephrine
Plasma
membrane
The amino acid-derived hormones epinephrine and
norepinephrine bind to beta-adrenergic receptors on the
plasma membrane of cells. Hormone binding to receptor
activates a G-protein, which in turn activates adenylyl
cyclase, converting ATP to cAMP. cAMP is a second
messenger that mediates a cell-specific response. An
enzyme called phosphodiesterase breaks down cAMP,
terminating the signal.
The specific response of a cell to a lipid insoluble hormone depends on the
type of receptors that are present on the plasma membrane and the substrate
molecules present in the cell cytoplasm. Cellular responses to hormone
binding of a receptor include altering membrane permeability and metabolic
pathways, stimulating synthesis of proteins and enzymes, and activating
hormone release.
Hormonal Regulation of Body Systems
Hormones have a wide range of effects and modulate many different body
processes. Two regulatory processes that will be examined here as examples
are regulation of the functions of the reproductive system, and regulation of
carbohydrate metabolism.
Hormonal Regulation of the Reproductive System
Regulation of the reproductive system is a process that requires the action
of hormones from the pituitary gland, the adrenal cortex, and the gonads.
During puberty in both males and females, the hypothalamus produces
gonadotropin-releasing hormone (GnRH), which stimulates the production
and release of follicle-stimulating hormone (FSH) and luteinizing
hormone (LH) from the anterior pituitary gland. These hormones regulate
the gonads (testes in males and ovaries in females) and therefore are called
gonadotropins. In both males and females, FSH stimulates gamete
production and LH stimulates production of hormones by the gonads. An
increase in gonad hormone levels inhibits GnRH production through a
negative feedback loop.
Regulation of the Male Reproductive System
In males, FSH stimulates the maturation of sperm cells. FSH production is
inhibited by the hormone inhibin, which is released by the testes. LH
stimulates production of the sex hormones (androgens) by the interstitial
cells of the testes and therefore is also called interstitial cell-stimulating
hormone.
The most widely known androgen in males is testosterone. Testosterone
promotes the production of sperm and masculine characteristics.
Note:
Everyday Connection
Professional baseball player Jason Giambi
publically admitted to, and apologized for,
his use of anabolic steroids supplied by a
trainer. (credit: Bryce Edwards)
Some athletes attempt to boost their performance by using artificial
hormones that enhance muscle performance. Anabolic steroids, a form of
the male sex hormone testosterone, are one of the most widely known
performance-enhancing drugs. Steroids are used to help build muscle mass.
Other hormones that are used to enhance athletic performance include
erythropoietin, which triggers the production of red blood cells, and human
growth hormone, which can help in building muscle mass. Most
performance enhancing drugs are illegal for non-medical purposes. They
are also banned by national and international governing bodies including
the International Olympic Committee, the U.S. Olympic Committee, the
National Collegiate Athletic Association, the Major League Baseball, and
the National Football League.
The side effects of synthetic hormones are often significant and non-
reversible, and in some cases, fatal. Androgens produce several
complications such as liver dysfunctions and liver tumors, prostate gland
enlargement, difficulty urinating, premature closure of epiphyseal
cartilages, testicular atrophy, infertility, and immune system depression.
The physiological strain caused by these substances is often greater than
what the body can handle, leading to unpredictable and dangerous effects
and linking their use to heart attacks, strokes, and impaired cardiac
function.
Regulation of the Female Reproductive System
In females, FSH stimulates development of egg cells, called ova, which
develop in structures called follicles. Follicle cells produce the hormone
inhibin, which inhibits FSH production. LH also plays a role in the
development of ova, induction of ovulation, and stimulation of estradiol and
progesterone production by the ovaries, as illustrated in [link]. Estradiol and
progesterone are steroid hormones that prepare the body for pregnancy.
Estradiol produces secondary sex characteristics in females, while both
estradiol and progesterone regulate the menstrual cycle.
GnRH secreted from
the hypothalmus
stimulates FSH
and LH production
Hypothalamus
Pituitary
in the pituitary. Estradiol,
progesterone
FSH and LH and inhibin are
stimulate follicle secreted from
growth in the ovaries.
the ovaries. Estradiol and
A surge in progesterone
LH triggers regulate
ovulation. female sex
characteristics
and the female
cycle. Inhibin
inhibits FSH
production by
the pituitary.
Uterus
Ovary
Hormonal regulation of the
female reproductive system
involves hormones from the
hypothalamus, pituitary, and
ovaries.
In addition to producing FSH and LH, the anterior portion of the pituitary
gland also produces the hormone prolactin (PRL) in females. Prolactin
stimulates the production of milk by the mammary glands following
childbirth. Prolactin levels are regulated by the hypothalamic hormones
prolactin-releasing hormone (PRH) and prolactin-inhibiting hormone (PIH),
which is now known to be dopamine. PRH stimulates the release of
prolactin and PIH inhibits it; this is a classic negative feedback loop.
The posterior pituitary releases the hormone oxytocin, which stimulates
uterine contractions during childbirth. The uterine smooth muscles are not
very sensitive to oxytocin until late in pregnancy when the number of
oxytocin receptors in the uterus peaks. Stretching of tissues in the uterus
and cervix stimulates oxytocin release during childbirth. Contractions
increase in intensity as blood levels of oxytocin rise via a positive feedback
mechanism until the birth is complete. Oxytocin also stimulates the
contraction of myoepithelial cells around the milk-producing mammary
glands. As these cells contract, milk is forced from the secretory alveoli into
milk ducts and is ejected from the breasts in milk ejection (“let-down’’)
reflex. Oxytocin release is stimulated by the suckling of an infant, which
triggers the synthesis of oxytocin in the hypothalamus and its release into
circulation at the posterior pituitary.
Hormonal Regulation of Carbohydrate Metabolism
Blood glucose levels vary widely over the course of a day as periods of
food consumption alternate with periods of fasting. Insulin and glucagon
are the two hormones primarily responsible for maintaining homeostasis of
blood glucose levels. Additional regulation is mediated by the thyroid
hormones.
Regulation of Blood Glucose Levels by Insulin and Glucagon
Cells of the body require nutrients in order to function, and these nutrients
are obtained through feeding. In order to manage nutrient intake, storing
excess intake and utilizing reserves when necessary, the body uses
hormones to moderate energy stores. Insulin is produced by the beta cells
of the pancreas, which are stimulated to release insulin as blood glucose
levels rise (for example, after a meal is consumed). Insulin lowers blood
glucose levels by enhancing the rate of glucose uptake and utilization by
target cells, which use glucose for ATP production. It also stimulates the
liver to convert glucose to glycogen, which is then stored by cells for later
use. Insulin also increases glucose transport into certain cells, such as
muscle cells, fat cells, and liver cells. This results from an insulin-mediated
increase in the number of glucose transporter proteins in plasma
membranes, which remove glucose from circulation by facilitated diffusion.
As insulin binds to its target cell via insulin receptors and signal
transduction, it triggers the cell to incorporate glucose transport proteins
into its membrane. Insulin also stimulates the conversion of glucose to fat in
adipocytes and the synthesis of proteins. These actions mediated by insulin
cause blood glucose concentrations to fall, called a hypoglycemic “low
sugar” effect, which inhibits further insulin release from beta cells through a
negative feedback loop.
When blood glucose levels decline below normal levels, for example
between meals or when glucose is utilized rapidly during exercise, the
hormone glucagon is released from the alpha cells of the pancreas.
Glucagon raises blood glucose levels, eliciting what is called a
hyperglycemic effect, by stimulating the breakdown of glycogen to glucose
in skeletal muscle cells and liver cells in a process called glycogenolysis.
Glucose can then be utilized as energy by muscle cells and released into
circulation by the liver cells. Glucagon also stimulates absorption of amino
acids from the blood by the liver, which then converts them to glucose. This
process of glucose synthesis is called gluconeogenesis. Glucagon also
stimulates adipose cells to release fatty acids into the blood. These actions
mediated by glucagon result in an increase in blood glucose levels to
normal homeostatic levels. Rising blood glucose levels inhibit further
glucagon release by the pancreas via a negative feedback mechanism. In
this way, insulin and glucagon work together to maintain homeostatic
glucose levels, as shown in [Link].
(” ‘N
‘|
Y
XN /
Insulin and glucagon regulate blood glucose levels via
negative feedback mechanisms.
Impaired insulin function can lead to a condition called diabetes mellitus,
the main symptoms of which are illustrated in [link]. This can be caused by
low levels of insulin production by the beta cells of the pancreas, or by
reduced sensitivity of tissue cells to insulin. This prevents glucose from
being absorbed by cells, causing high levels of blood glucose, or
hyperglycemia (high sugar). High blood glucose levels make it difficult for
the kidneys to recover all the glucose from nascent urine, resulting in
glucose being lost in urine. High glucose levels also result in less water
being reabsorbed by the kidneys, causing high amounts of urine to be
produced; this may result in dehydration. Over time, high blood glucose
levels can cause nerve damage to the eyes and peripheral body tissues, as
well as damage to the kidneys and cardiovascular system. Oversecretion of
insulin can cause hypoglycemia, low blood glucose levels. This causes
insufficient glucose availability to cells, often leading to muscle weakness,
and can sometimes cause unconsciousness or death if left untreated.
Central nervous
system
* Lethargy
* Stupor
* Excessive thirst
* Excessive hunger
Eyes
Blurred vision
Breath
Systemic + Smell of acetone
* Weight loss
Gastric
+ Nausea
+ Vomiting
+ Abdominal
pain
Urinary
* Frequent
urination
_ Glucose
In urine
The main symptoms of
diabetes are shown. (credit:
modification of work by
Mikael Haggstr6m)
Respiratory
* Hyperventilati
Endocrine Glands
Both the endocrine and nervous systems use chemical signals to
communicate and regulate the body's physiology. The endocrine system
releases hormones that act on target cells to regulate development, growth,
energy metabolism, reproduction, and many behaviors. The nervous system
releases neurotransmitters or neurohormones that regulate neurons, muscle
cells, and endocrine cells. Because the neurons can regulate the release of
hormones, the nervous and endocrine systems work in a coordinated
manner to regulate the body's physiology.
Hypothalamic-Pituitary Axis
The hypothalamus in vertebrates integrates the endocrine and nervous
systems. The hypothalamus is an endocrine organ located in the
diencephalon of the brain. It receives input from the body and other brain
areas and initiates endocrine responses to environmental changes. The
hypothalamus acts as an endocrine organ, synthesizing hormones and
transporting them along axons to the posterior pituitary gland. It synthesizes
and secretes regulatory hormones that control the endocrine cells in the
anterior pituitary gland. The hypothalamus contains autonomic centers that
control endocrine cells in the adrenal medulla via neuronal control.
The pituitary gland, sometimes called the hypophysis or “master gland” is
located at the base of the brain in the sella turcica, a groove of the sphenoid
bone of the skull, illustrated in [link]. It is attached to the hypothalamus via
a stalk called the pituitary stalk (or infundibulum). The anterior portion of
the pituitary gland is regulated by releasing or release-inhibiting hormones
produced by the hypothalamus, and the posterior pituitary receives signals
via neurosecretory cells to release hormones produced by the
hypothalamus. The pituitary has two distinct regions—the anterior pituitary
and the posterior pituitary—which between them secrete nine different
peptide or protein hormones. The posterior lobe of the pituitary gland
contains axons of the hypothalamic neurons.
\ Ma Pituitary stalk
Cerebellum An = == oN
iy } . \
Hypothalamus
Brain stem
———— Spinal cord Anterior pituitary Posterior pituitary
(a) (b)
The pituitary gland is located at (a) the base of the brain
and (b) connected to the hypothalamus by the pituitary
stalk. (credit a: modification of work by NCI; credit b:
modification of work by Gray’s Anatomy)
Thyroid Gland
The thyroid gland is located in the neck, just below the larynx and in front
of the trachea, as shown in [link]. It is a butterfly-shaped gland with two
lobes that are connected by the isthmus. It has a dark red color due to its
extensive vascular system. When the thyroid swells due to dysfunction, it
can be felt under the skin of the neck.
Thyroid gland
Trachea
This illustration shows the
location of the thyroid
gland.
Thyroid follicle cells synthesize the hormone thyroxine, which is also
known as Ty because it contains four atoms of iodine, and triiodothyronine,
also known as T3 because it contains three atoms of iodine. Follicle cells are
stimulated to release stored T3 and Ty, by thyroid stimulating hormone
(TSH), which is produced by the anterior pituitary. These thyroid hormones
increase the rates of mitochondrial ATP production.
A third hormone, calcitonin, is produced by parafollicular cells of the
thyroid either releasing hormones or inhibiting hormones. Calcitonin
release is not controlled by TSH, but instead is released when calcium ion
concentrations in the blood rise. Calcitonin functions to help regulate
calcium concentrations in body fluids. It acts in the bones to inhibit
osteoclast activity and in the kidneys to stimulate excretion of calcium. The
combination of these two events lowers body fluid levels of calcium.
Parathyroid Glands
Most people have four parathyroid glands; however, the number can vary
from two to six. These glands are located on the posterior surface of the
thyroid gland, as shown in [link]. Normally, there is a superior gland and an
inferior gland associated with each of the thyroid’s two lobes. Each
parathyroid gland is covered by connective tissue and contains many
secretory cells that are associated with a capillary network.
— Thyroid gland
Parathyroid gland
The parathyroid glands are
located on the posterior of the
thyroid gland. (credit:
modification of work by
NCI)
The parathyroid glands produce parathyroid hormone (PTH). PTH increases
blood calcium concentrations when calcium ion levels fall below normal.
PTH (1) enhances reabsorption of Ca** by the kidneys, (2) stimulates
osteoclast activity and inhibits osteoblast activity, and (3) it stimulates
synthesis and secretion of calcitriol by the kidneys, which enhances Ca?*
absorption by the digestive system. PTH and calcitonin work in opposition
to one another to maintain homeostatic Ca** levels in body fluids.
Adrenal Glands
The adrenal glands are associated with the kidneys; one gland is located on
top of each kidney as illustrated in [link]. The adrenal glands consist of an
outer adrenal cortex and an inner adrenal medulla. These regions secrete
different hormones.
Adrenal gland
Kidney
The location of the adrenal
glands on top of the kidneys
is shown. (credit:
modification of work by
NCI)
Adrenal Cortex
The adrenal cortex is made up of layers of epithelial cells and associated
capillary networks. This gland produces mineralcorticoids, glucocorticoids,
and androgens. The main mineralocorticoid (a class of steroid hormones
that regulate salt and water balance) is aldosterone, which regulates the
concentration of Na”* ions in urine, sweat, pancreas, and saliva. Aldosterone
release from the adrenal cortex is stimulated by a decrease in blood
concentrations of sodium ions, blood volume, or blood pressure, or by an
increase in blood potassium levels.
The three main glucocorticoids (steroid hormones that regulate glucose
metabolism) are cortisol, corticosterone, and cortisone. The glucocorticoids
stimulate the synthesis of glucose. and can also enhance gluconeogenesis
(conversion of a non-carbohydrate to glucose) by liver cells. They also
promote the release of fatty acids from adipose tissue. These hormones
increase blood glucose levels to maintain levels within a normal range
between meals. These hormones are secreted in response to ACTH, and
levels are regulated by negative feedback.
Androgens are sex hormones that promote masculinity. They are produced
in small amounts by the adrenal cortex in both males and females. They do
not affect sexual characteristics and may supplement sex hormones released
from the gonads.
Adrenal Medulla
The adrenal medulla contains two types of secretory cells: one that
produces epinephrine (adrenaline) and another that produces norepinephrine
(noradrenaline). Epinephrine is the primary adrenal medulla hormone
accounting for 75 to 80 percent of its secretions. Epinephrine and
norepinephrine increase heart rate, breathing rate, cardiac muscle
contractions, blood pressure, and blood glucose levels. They also accelerate
the breakdown of glucose in skeletal muscles and stored fats in adipose
tissue.
The release of epinephrine and norepinephrine is stimulated by neural
impulses from the sympathetic nervous system. Neural impulses,
originating from the hypothalamus in response to stress, release these
hormones to prepare the body for the fight-or-flight response.
Pancreas
The pancreas, illustrated in [link], is an elongated organ that is located
between the stomach and the proximal portion of the small intestine. It
contains both exocrine cells that excrete digestive enzymes and endocrine
cells that release hormones. It is sometimes referred to as a heterocrine
gland because it has both endocrine and exocrine functions.
Stomach
Gall bladder
Common bile duct
Duodenum Pancreas
The pancreas is found
underneath the stomach and
points toward the spleen.
(credit: modification of work
by NCI)
The endocrine cells of the pancreas form clusters called pancreatic islets or
the islets of Langerhans, as visible in the micrograph shown in [link]. The
pancreatic islets contain two primary cell types: alpha cells, which produce
the hormone glucagon, and beta cells, which produce the hormone insulin.
These hormones regulate blood glucose levels. As blood glucose levels
decline, alpha cells release glucagon to raise the blood glucose levels by
increasing rates of glycogen breakdown and glucose release by the liver.
When blood glucose levels rise, such as after a meal, beta cells release
insulin to lower blood glucose levels by increasing the rate of glucose
uptake in most body cells, and by increasing glycogen synthesis in skeletal
muscles and the liver. Together, glucagon and insulin regulate blood
glucose levels.
The islets of Langerhans are
clusters of endocrine cells
found in the pancreas; they
stain lighter than surrounding
cells. (credit: modification of
work by Muhammad T. Tabiin,
Christopher P. White, Grant
Morahan, and Bernard E. Tuch;
scale-bar data from Matt
Russell)
Pineal Gland
The pineal gland produces melatonin. The rate of melatonin production is
affected by the photoperiod (amount of light in a 24-hour period). Nerves
from the visual pathways innervate the pineal gland. During the day (light),
little melatonin is produced; however, melatonin production increases
during the night (dark). In some mammals, melatonin has an inhibitory
affect on reproductive functions by decreasing production and maturation of
sperm, oocytes, and reproductive organs. Lastly, melatonin is involved in
biological rhythms, particularly circadian rhythms such as the sleep-wake
cycle and eating habits.
Gonads
The gonads—the male testes and female ovaries—produce steroid
hormones. The testes produce androgens, testosterone being the most
prominent, which allow for the development of secondary sex
characteristics and the production of sperm cells. The ovaries produce
estradiol and progesterone, which cause secondary sex characteristics and
prepare the body for childbirth.
Endocrine Glands and their Associated Hormones
Endocrine
Gland
Hypothalamus
Pituitary
(Anterior)
Associated
Hormones
releasing and
inhibiting
hormones
antidiuretic
hormone (ADH)
growth hormone
(GH)
prolactin (PRL)
thyroid stimulating
hormone (TSH)
adrenocorticotropic
hormone (ACTH)
follicle-stimulating
hormone (FSH)
Effect
regulate hormone release
from pituitary gland;
produce oxytocin;
produce uterine
contractions and milk
secretion in females
water reabsorption from
kidneys; vasoconstriction
to increase blood
pressure
promotes growth of body
tissues, protein synthesis;
metabolic functions
promotes milk
production
stimulates thyroid
hormone release
stimulates hormone
release by adrenal
cortex, glucocorticoids
stimulates gamete
production (both ova and
sperm); secretion of
estradiol
Endocrine Glands and their Associated Hormones
Endocrine
Gland
Pituitary
(Posterior)
Thyroid
Parathyroid
Associated
Hormones
luteinizing
hormone (LH)
melanocyte-
stimulating
hormone (MSH)
antidiuretic
hormone (ADH)
oxytocin
thyroxine,
triiodothyronine
calcitonin
parathyroid
hormone (PTH)
Effect
stimulates androgen
production by gonads;
ovulation, secretion of
progesterone
stimulates melanocytes
of the skin increasing
melanin pigment
production.
stimulates water
reabsorption by kidneys
stimulates uterine
contractions during
childbirth; milk ejection;
stimulates ductus
deferens and prostate
gland contraction during
emission
stimulate and maintain
metabolism; growth and
development
reduces blood Ca2*
levels
increases blood Ca2*
levels
Endocrine Glands and their Associated Hormones
Endocrine
Gland
Adrenal
(Cortex)
Adrenal
(Medulla)
Pancreas
Pineal gland
Testes
Associated
Hormones
aldosterone
cortisol,
corticosterone,
cortisone
epinephrine,
norepinephrine
insulin
glucagon
melatonin
androgens
Effect
increases blood Na*
levels; increase K*
secretion
increase blood glucose
levels; anti-inflammatory
effects
stimulate fight-or-flight
response; increase blood
gluclose levels; increase
metabolic activities
reduces blood glucose
levels
increases blood glucose
levels
regulates some
biological rhythms and
protects CNS from free
radicals
regulate, promote,
increase or maintain
sperm production; male
secondary sexual
characteristics
Endocrine Glands and their Associated Hormones
Endocrine Associated
Gland Hormones Effect
promotes uterine lining
growth; female
estrogen
secondary sexual
Ovaries characteristics
promote and maintain
progestins
uterine lining growth
Digestive System Regulation
Introduction
"The digestive canal is in its task a complete chemical factory. The raw
material passes through a long series of institutions in which it is subjected
to certain mechanical and, mainly, chemical processing, and then, through
innumerable side-streets, it is brought into the depot of the body. Aside
from this basic series of institutions, along which the raw material moves,
there is a series of lateral chemical manufactories, which prepare certain
reagents for the appropriate processing of the raw material." Ivan Petrovich
Pavlov, Speech to the Society of Russian Physicians, Dec. 1874
Pavlov's pioneering work, showing that dogs can associate the ringing of a
bell with the imminent delivery of food, pointed the way toward our current
understanding of the coordinated responses that regulate the digestive
system. The brain is the control center for the sensation of hunger and
satiety. The functions of the digestive system are regulated through neural
and hormonal responses.
Neural Responses to Food
In reaction to the smell, sight, or thought of food, like that shown in [link],
the first hormonal response is that of salivation. The salivary glands secrete
more saliva in response to the stimulus presented by food in preparation for
digestion. Simultaneously, the stomach begins to produce hydrochloric acid
to digest the food. Recall that the peristaltic movements of the esophagus
and other organs of the digestive tract are under the control of the brain.
The brain prepares these muscles for movement as well. When the stomach
is full, the part of the brain that detects satiety signals fullness. There are
three overlapping phases of gastric control—the cephalic phase, the gastric
phase, and the intestinal phase—each requires many enzymes and is under
neural control as well.
Seeing a plate of food triggers the
secretion of saliva in the mouth and
the production of HCL in the stomach.
(credit: Kelly Bailey)
Digestive Phases
The response to food begins even before food enters the mouth. The first
phase of ingestion, called the cephalic phase, is controlled by the neural
response to the stimulus provided by food. All aspects—such as sight,
sense, and smell—trigger the neural responses resulting in salivation and
secretion of gastric juices. The gastric and salivary secretion in the cephalic
phase can also take place due to the thought of food. Right now, if you think
about a piece of chocolate or a crispy potato chip, the increase in salivation
is a cephalic phase response to the thought. The central nervous system
prepares the stomach to receive food.
The gastric phase begins once the food arrives in the stomach. It builds on
the stimulation provided during the cephalic phase. Gastric acids and
enzymes process the ingested materials. The gastric phase is stimulated by
(1) distension of the stomach, (2) a decrease in the pH of the gastric
contents, and (3) the presence of undigested material. This phase consists of
local, hormonal, and neural responses. These responses stimulate secretions
and powerful contractions.
The intestinal phase begins when chyme enters the small intestine
triggering digestive secretions. This phase controls the rate of gastric
emptying. In addition to gastric emptying, when chyme enters the small
intestine, it triggers other hormonal and neural events that coordinate the
activities of the intestinal tract, pancreas, liver, and gallbladder.
Hormonal Responses to Food
The endocrine system controls the response of the various glands in the
body and the release of hormones at the appropriate times.
One of the important factors under hormonal control is the stomach acid
environment. During the gastric phase, the hormone gastrin is secreted by
G cells in the stomach in response to the presence of proteins in the
stomach contents. Gastrin stimulates the release of hydrochloric acid (HCl),
which aids in the digestion of the proteins. However, when the stomach is
emptied, the acidic environment no longer needs to be maintained, and a
hormone called somatostatin stops the release of hydrochloric acid. This is
a good example of a negative feedback system: proteins in the stomach
cause a response that results in elimination of proteins from the stomach
contents, via the actions of two counteracting hormones.
In the duodenum, digestive secretions from the liver, pancreas, and
gallbladder play an important role in digesting chyme during the intestinal
phase. In order to neutralize the acidic chyme, a hormone called secretin
stimulates the pancreas to produce alkaline bicarbonate solution and deliver
it to the duodenum. Secretin acts in tandem with another hormone called
cholecystokinin (CCK). Not only does CCK stimulate the pancreas to
produce the requisite pancreatic juices, it also stimulates the gallbladder to
release bile into the duodenum. This is another negative feedback loop;
what parameters are being sensed and regulated?
Another level of hormonal control occurs in response to the composition of
food. Foods high in lipids take a long time to digest. A hormone called
gastric inhibitory peptide is secreted by the small intestine to slow down the
peristaltic movements of the intestine to allow fatty foods more time to be
digested and absorbed.
Understanding the hormonal control of the digestive system is an important
area of ongoing research. Scientists are exploring the role of each hormone
in the digestive process and developing ways to target these hormones.
Advances could lead to knowledge that may help to battle the obesity
epidemic.
How Animals Reproduce
Introduction
" Reproduction is so primitive and fundamental a function of vital
organisms that the mechanism by which it is assured is highly complex and
not yet clearly understood. It is not necessarily connected with sex, nor is
sex necessarily connected with reproduction." Henry Havelock Ellis, in
Psychology of Sex, 1933
Some animals produce offspring through asexual reproduction while other
animals produce offspring through sexual reproduction. Both methods have
advantages and disadvantages. Asexual reproduction produces offspring
that are genetically identical to the parent because the offspring are all
clones of the original parent. A single individual can produce offspring
asexually and large numbers of offspring can be produced quickly; these are
two advantages that asexually reproducing organisms have over sexually
reproducing organisms. In a stable or predictable environment, asexual
reproduction is an effective means of reproduction because all the offspring
will be adapted to that environment. In an unstable or unpredictable
environment, species that reproduce asexually may be at a disadvantage
because all the offspring are genetically identical and may not be adapted to
different conditions.
During sexual reproduction, the genetic material of two individuals is
combined to produce genetically diverse offspring that differ from their
parents. The genetic diversity of sexually produced offspring is thought to
give sexually reproducing individuals greater fitness because more of their
offspring may survive and reproduce in an unpredictable or changing
environment. Species that reproduce sexually (and have separate sexes)
must maintain two different types of individuals, males and females. Only
half the population (females) can produce the offspring, so fewer offspring
will be produced when compared to asexual reproduction. This is a
disadvantage of sexual reproduction compared to asexual reproduction.
Asexual Reproduction
Asexual reproduction occurs in prokaryotic microorganisms (bacteria and
archaea) and in many eukaryotic, single-celled and multi-celled organisms,
both plants and animals. There are several ways that animals reproduce
asexually, the details of which vary among individual species.
Fission
Fission, also called binary fission, occurs in some invertebrate, multi-celled
organisms. It is in some ways analogous to the process of binary fission of
single-celled prokaryotic organisms. The term fission is applied to instances
in which an organism appears to split itself into two parts and, if necessary,
regenerate the missing parts of each new organism. For example, some
flatworms, such as Dugesia dorotocephala, are able to separate their bodies
into head and tail regions and then regenerate the missing half in each of the
two new organisms. Sea anemones (Cnidaria), such as species of the genus
Anthopleura ({link]), will divide along the oral-aboral axis, and sea
cucumbers (Echinodermata) of the genus Holothuria, will divide into two
halves across the oral-aboral axis and regenerate the other half in each of
the resulting individuals.
The Anthopleura artemisia
sea anemone can reproduce
through fission.
Budding
Budding is a form of asexual reproduction that results from the outgrowth
of a part of the body leading to a separation of the “bud” from the original
organism and the formation of two individuals, one smaller than the other.
Budding occurs commonly in some invertebrate animals such as hydras and
corals. In hydras, a bud forms that develops into an adult and breaks away
from the main body ([link]).
(a) Hydra reproduce asexually through
budding: a bud forms on the tubular body of an
adult hydra, develops a mouth and tentacles,
and then detaches from its parent. The new
hydra is fully developed and will find its own
location for attachment. (b) Some coral, such
as the Lophelia pertusa shown here, can
reproduce through budding. (credit b:
modification of work by Ed Bowlby,
NOAA/Olympic Coast NMS;
NOAA/OAR/Office of Ocean Exploration)
Fragmentation
Fragmentation is the breaking of an individual into parts followed by
regeneration. If the animal is capable of fragmentation, and the parts are big
enough, a separate individual will regrow from each part. Fragmentation
may occur through accidental damage, damage from predators, or as a
natural form of reproduction. Reproduction through fragmentation is
observed in sponges, some cnidarians, turbellarians, echinoderms, and
annelids. In some sea stars, a new individual can be regenerated from a
broken arm and a piece of the central disc. This sea star ({link]) is in the
process of growing a complete sea star from an arm that has been cut off.
Fisheries workers have been known to try to kill the sea stars eating their
clam or oyster beds by cutting them in half and throwing them back into the
ocean. Unfortunately for the workers, the two parts can each regenerate a
new half, resulting in twice as many Sea stars to prey upon the oysters and
clams.
(b)
(a) Linckia multifora is a species of sea star
that can reproduce asexually via fragmentation.
In this process, (b) an arm that has been shed
grows into a new Sea Star. (credit a:
modifiction of work by Dwayne Meadows,
NOAA/NMEFS/OPR)
Parthenogenesis
Parthenogenesis is a form of asexual reproduction in which an egg
develops into an individual without being fertilized. The resulting offspring
can be either haploid or diploid, depending on the process and the particular
species. Parthenogenesis occurs in invertebrates such as water fleas,
rotifers, aphids, stick insects, and ants, wasps, and bees. Ants, bees, and
wasps use parthenogenesis to produce haploid males (drones). The diploid
females (workers and queens) are the result of a fertilized egg.
Some vertebrate animals—including some reptiles, amphibians, and fish—
also reproduce through parthenogenesis. Parthenogenesis has been observed
in species in which the sexes were separated in terrestrial or marine zoos.
Two female Komodo dragons, a hammerhead shark, and a blacktop shark
have produced parthenogenic young, even when the females have been
isolated from males. It is possible that these instances of parthenogenesis
occurred in response to unusual circumstances stemming from captivity,
and would normally not occur.
Sexual Reproduction
Sexual reproduction is the combination of reproductive cells from two
individuals, each contributing a haploid gamete, to generate genetically
unique offspring. The nature of the individuals that produce the two kinds
of gametes can vary, having for example separate sexes or both sexes in
each individual.
Hermaphroditism
Hermaphroditism occurs in animals in which one individual has both male
and female reproductive systems. Invertebrates such as earthworms, slugs,
tapeworms, and snails ([link]) are often hermaphroditic. Hermaphrodites
may self-fertilize, but typically they will mate with another of their species,
fertilizing each other and both producing offspring. Self-fertilization is
more common in animals that have limited mobility or are not motile, such
as barnacles and clams. Many species have specific mechanisms in place to
prevent self-fertilization, because it is an extreme form of inbreeding and
usually produces less fit offspring.
Many (a) snails are hermaphrodites. When two
individuals (b) mate, they can produce up to
100 eggs each. (credit a: modification of work
by Assaf Shtilman; credit b: modification of
work by "Schristia"/Flickr)
Fertilization
The fusion of a sperm and an egg is a process called fertilization. This can
occur either inside (internal fertilization) or outside (external fertilization)
the body of the female. Humans provide an example of the former, whereas
frog reproduction is an example of the latter.
External Fertilization
External fertilization usually occurs in aquatic environments where both
eggs and sperm are released into the water. After the sperm reaches the egg,
fertilization takes place. Most external fertilization happens during the
process of spawning where one or several females release their eggs and the
male(s) release sperm in the same area, at the same time. The spawning
may be triggered by environmental signals, such as water temperature or
the length of daylight. Nearly all fish spawn, as do crustaceans (such as
crabs and shrimp), mollusks (such as oysters), squid, and echinoderms
(such as sea urchins and sea cucumbers). Frogs, corals, mayflies, and
mosquitoes also spawn ((link]).
During sexual reproduction in
toads, the male grasps the female
from behind and externally
fertilizes the eggs as they are
deposited. (credit: Bernie Kohl)
Internal Fertilization
Internal fertilization occurs most often in terrestrial animals, although some
aquatic animals also use this method. Internal fertilization may occur by the
male directly depositing sperm in the female during mating. It may also
occur by the male depositing sperm in the environment, usually in a
protective structure, which a female picks up to deposit the sperm in her
reproductive tract. There are three ways that offspring are produced
following internal fertilization. In oviparity, fertilized eggs are laid outside
the female’s body and develop there, receiving nourishment from the yolk
that is a part of the egg ([link]a). This occurs in insects, some bony fish,
some reptiles, a few cartilaginous fish, some amphibians, a few mammals,
and all birds. Most non-avian reptiles and insects produce leathery eggs,
while birds and some turtles produce eggs with high concentrations of
calcium carbonate in the shell, making them hard. Chicken eggs are an
example of a hard shell. The eggs of the egg-laying mammals such as the
platypus and echidna are leathery.
In ovoviparity, fertilized eggs are retained in the female, and the embryo
obtains its nourishment from the egg’s yolk. The eggs are retained in the
female’s body until they hatch inside of her, or she lays the eggs right
before they hatch. This process helps protect the eggs until hatching. This
occurs in some bony fish (like the platyfish Xiphophorus maculatus,
[link]b), some sharks, lizards, some snakes (garter snake Thamnophis
sirtalis), Some vipers, and some invertebrate animals (Madagascar hissing
cockroach Gromphadorhina portentosa).
In viviparity the young are born alive. They obtain their nourishment from
the female and are born in varying states of maturity. This occurs in most
mammals ([link]c), some cartilaginous fish, and a few reptiles.
(a) (b) (c)
In (a) oviparity, young develop in eggs outside the
female body, as with these Harmonia axydridis beetles
hatching. Some aquatic animals, like this (b) pregnant
Xiphophorus maculatus are ovoviparous, with the egg
developing inside the female and nutrition supplied
primarily from the yolk. In mammals, nutrition is
supported by the placenta, as was the case with this (c)
newborn squirrel. (credit b: modification of work by
Gourami Watcher; credit c: modification of work by
"audreyjm529"/Flickr)
Hormonal Control of Reproduction
In the animal kingdom there are many interesting examples of reproductive
strategies, and hormones are involved in regulating all of those. Rather than
attempt to cover the wide diversity of strategies and hormones, we will
concentrate on the hormonal control of reproduction in a single species,
Homo sapiens.
The human male and female reproductive cycles are controlled by the
interaction of hormones from the hypothalamus and anterior pituitary with
hormones from reproductive tissues and organs. In both sexes, the
hypothalamus monitors and causes the release of hormones from the
anterior pituitary gland. When the reproductive hormone is required, the
hypothalamus sends a gonadotropin-releasing hormone (GnRH) to the
anterior pituitary. This causes the release of follicle stimulating hormone
(FSH) and luteinizing hormone (LH) from the anterior pituitary into the
blood. Although these hormones are named after their functions in female
reproduction, they are produced in both sexes and play important roles in
controlling reproduction. Other hormones have specific functions in the
male and female reproductive systems.
Male Hormones
At the onset of puberty, the hypothalamus causes the release of FSH and
LH into the male system for the first time. FSH enters the testes and
stimulates the Sertoli cells located in the walls of the seminiferous tubules
to begin promoting spermatogenesis ([link]). LH also enters the testes and
stimulates the interstitial cells of Leydig, located in between the walls of the
seminiferous tubules, to make and release testosterone into the testes and
the blood.
Testosterone stimulates spermatogenesis. This hormone is also responsible
for the secondary sexual characteristics that develop in the male during
adolescence. The secondary sex characteristics in males include a
deepening of the voice, the growth of facial, axillary, and pubic hair, an
increase in muscle bulk, and the beginnings of the sex drive.
Pituitary hormone effects: [Hypothalamus |
LH and FSH stimulate spermatogenesis
and testosterone secretion by the testes. y GnRH
Inhibin
Testosterone
Se oe Nate Testes hormone effects:
Bete oe Testosterone and inhibin inhibit
the secretion of GnRH by the
Leydig cells hypothalamus and LH and FSH
by the pituitary.
Hormones control sperm production in a negative feedback
system.
LH
A negative feedback system occurs in the male with rising levels of
testosterone acting on the hypothalamus and anterior pituitary to inhibit the
release of GnRH, FSH, and LH. In addition, the Sertoli cells produce the
hormone inhibin, which is released into the blood when the sperm count is
too high. This inhibits the release of GnRH and FSH, which will cause
spermatogenesis to slow down. If the sperm count reaches a low of 20
million/mL, the Sertoli cells cease the release of inhibin, and the sperm
count increases.
Female Hormones
The control of reproduction in females is more complex. The female
reproductive cycle is divided into the ovarian cycle and the menstrual cycle.
The ovarian cycle governs the preparation of endocrine tissues and release
of eggs, while the menstrual cycle governs the preparation and maintenance
of the uterine lining ({link]). These cycles are coordinated over a 22—32 day
cycle, with an average length of 28 days.
As with the male, the GnRH from the hypothalamus causes the release of
the hormones FSH and LH from the anterior pituitary. In addition, estrogen
and progesterone are released from the developing follicles. As with
testosterone in males, estrogen is responsible for the secondary sexual
characteristics of females. These include breast development, flaring of the
hips, and a shorter period for bone growth.
The Ovarian Cycle and the Menstrual Cycle
The ovarian and menstrual cycles are regulated by hormones of the
hypothalamus, pituitary, and ovaries ([link]). The ebb and flow of the
hormones causes the ovarian and menstrual cycles to advance. The ovarian
and menstrual cycles occur concurrently. The first half of the ovarian cycle
is the follicular phase. Slowly rising levels of FSH cause the growth of
follicles on the surface of the ovary. This process prepares the egg for
ovulation. As the follicles grow, they begin releasing estrogen. The first few
days of this cycle coincide with menstruation or the sloughing off of the
functional layer of the endometrium in the uterus. After about five days,
estrogen levels rise and the menstrual cycle enters the proliferative phase.
The endometrium begins to regrow, replacing the blood vessels and glands
that deteriorated during the end of the last cycle.
| Follicular phase Il Ovulation
Pituitary hormone Pituitary hormone
effect: LH and FSH effect: LH and FSH
stimulate several GnRH stimulate maturation GnRH
follicles to grow. of one of the
growing follicles.
Estrogen
Ovarian Ovarian
hormone hormone
effects: effects:
Dominant follicle
produces low
levels of estrogen,
which:
e Stimulate GnRH
secretion by the
hypothalamus.
FSH Follicles produce
low levels of
FSH
H estrogen that LH
Estrogen inhibit GaRH
secretion by
| Fotis | the hypothalamus,
keeping LH and
FSH levels low. LH and FSH
Estrogen Cause endometrial Estrogen _ levels rise,
arteries to constrict resulting in
due to low levels, ovulation about
resulting in a day later.
endometium| menstruation. endometium| e Cause the
endometrium
to thicken.
Ill Luteal phase
Pituitary hormone
effect: LH stimulates
formation of a corpus GnRH
luteum from follicular
tissue left behind after
ovulation.
Ovarian
hormone
effects:
The corpus
luteum secretes
LH Zp
Progesterone estrogen and
progesterone that
Corpus luteum e Block GnRH
production by the
hypothalamus
Estrogen and LH and
| FSH production
Progesterone by the pituitary.
aa Cause the
| Endometium | endometrium to
further develop.
The ovarian and menstrual cycles of female reproduction
are regulated by hormones produced by the
hypothalamus, pituitary, and ovaries.
Estrogen
Just prior to the middle of the cycle (approximately day 14), the high level
of estrogen causes FSH and especially LH to rise rapidly then fall. The
spike in LH causes the most mature follicle to rupture and release its egg.
This is ovulation. The follicles that did not rupture degenerate and their
eggs are lost. The level of estrogen decreases when the extra follicles
degenerate.
Following ovulation, the ovarian cycle enters its luteal phase and the
menstrual cycle enters its secretory phase, both of which run from about
day 15 to 28. The luteal and secretory phases refer to changes in the
ruptured follicle. The cells in the follicle undergo physical changes and
produce a structure called a corpus luteum. The corpus luteum produces
estrogen and progesterone. The progesterone facilitates the regrowth of the
uterine lining and inhibits the release of further FSH and LH. The uterus is
being prepared to accept a fertilized egg, should it occur during this cycle.
The inhibition of FSH and LH prevents any further eggs and follicles from
developing, while the progesterone is elevated. The level of estrogen
produced by the corpus luteum increases to a steady level for the next few
days.
If no fertilized egg is implanted into the uterus, the corpus luteum
degenerates and the levels of estrogen and progesterone decrease. The
endometrium begins to degenerate as the progesterone levels drop,
initiating the next menstrual cycle. The decrease in progesterone also allows
the hypothalamus to send GnRH to the anterior pituitary, releasing FSH and
LH and starting the cycles again.
Gestation
Pregnancy begins with the fertilization and implantation of an egg and
continues through to the birth of the individual. The length of time of
gestation, or the gestation period, in humans is 266 days and is similar in
other great apes. Gestation periods in other animals range from 12-13 days
in the American opossum to the 660 day gestation period of the African
elephant.
Within 24 hours of fertilization, the egg nucleus has finished meiosis and
the egg and sperm nuclei fuse. With fusion, the cell is known as a zygote.
The zygote initiates cleavage and the developing embryo travels through
the oviduct to the uterus. The developing embryo must implant into the wall
of the uterus within seven days, or it will deteriorate and die. The outer
layers of the developing embryo or blastocyst grow into the endometrium
by digesting the endometrial cells, and healing of the endometrium closes
up the blastocyst into the tissue. Another layer of the blastocyst, the
chorion, begins releasing a hormone called human beta chorionic
gonadotropin (B-HCG), which makes its way to the corpus luteum and
keeps that structure active. This ensures adequate levels of progesterone
that will maintain the endometrium of the uterus for the support of the
developing embryo. Pregnancy tests determine the level of B-HCG in urine
or serum. If the hormone is present, the test is positive.
The gestation period is divided into three equal periods or trimesters.
During the first two-to-four weeks of the first trimester, nutrition and waste
are handled by the endometrial lining through diffusion. As the trimester
progresses, the outer layer of the embryo begins to merge with the
endometrium, and the placenta forms. The placenta takes over the nutrient
and waste requirements of the embryo and fetus, with the mother’s blood
passing nutrients to the placenta and removing waste from it. Chemicals
from the fetus, such as bilirubin, are processed by the mother’s liver for
elimination. Some of the mother’s immunoglobulins will pass through the
placenta, providing passive immunity against some potential infections.
Internal organs and body structures begin to develop during the first
trimester. By five weeks, limb buds, eyes, the heart, and liver have been
basically formed. By eight weeks, the term fetus applies, and the body is
essentially formed ({link]a). The individual is about five centimeters (two
inches) in length and many of the organs, such as the lungs and liver, are
not yet functioning. Exposure to any toxins is especially dangerous during
the first trimester, as all of the body’s organs and structures are going
through initial development. Anything that interferes with chemical
signaling during that development can have a severe effect on the fetus’
survival.
(b)
(a) Fetal development is shown at nine weeks
gestation. (b) This fetus is just entering the second
trimester, when the placenta takes over more of the
functions performed as the baby develops. (c)
There is rapid fetal growth during the third
trimester. (credit a: modification of work by Ed
Uthman; credit b: modification of work by
National Museum of Health and Medicine; credit
c: modification of work by Gray’s Anatomy)
During the second trimester, the fetus grows to about 30 cm (about 12
inches) ([link]b). It becomes active and the mother usually feels the first
movements. All organs and structures continue to develop. The placenta has
taken over the functions of nutrition and waste elimination and the
production of estrogen and progesterone from the corpus luteum, which has
degenerated. The placenta will continue functioning up through the delivery
of the baby. During the third trimester, the fetus grows to 3 to 4 kg (6.5-8.5
Ibs.) and about 50 cm (19—20 inches) long ({link]c). This is the period of the
most rapid growth during the pregnancy as all organ systems continue to
grow and develop.
Labor is the name given to the muscular contractions that expel the fetus
and placenta from the uterus. Toward the end of the third trimester, estrogen
causes receptors on the uterine wall to develop and bind the hormone
oxytocin. At this time, the fetus usually reorients, facing forward and down
with the back or crown of the head pushing on the cervix (uterine opening).
This causes the cervix to stretch and nerve impulses are sent to the
hypothalamus, which signals the release of oxytocin from the posterior
pituitary. Oxytocin causes smooth muscle in the uterine wall to contract. At
the same time, the placenta releases prostaglandins into the uterus,
increasing the contractions. A positive feedback relay occurs between the
uterus, hypothalamus, and the posterior pituitary to assure an adequate
supply of oxytocin. As more smooth muscle cells are recruited, the
contractions increase in intensity and force. As noted previously, this is a
good example of a positive feedback loop — the stimulus causes the
production of a hormone that increases the stimulus.
There are three stages to labor. During stage one, the cervix thins and
dilates. This is necessary for the baby and placenta to be expelled during
birth. The cervix will eventually dilate to about 10 cm. During stage two,
the baby is expelled from the uterus. The uterus contracts and the mother
pushes as she compresses her abdominal muscles to aid the delivery. The
last stage is the passage of the placenta after the baby has been born and the
organ has completely disengaged from the uterine wall. If labor should stop
before stage two is reached, synthetic oxytocin, known as Pitocin, can be
administered to restart and maintain labor.
The Integumentary System
Introduction
I am not this hair, I am not this skin, I am the soul that lives within. - Jalal
ad-Din Rumi
Rumi's line plays on the unusual focus on hair color and skin color that
humans have had for many centuries, and asks us to look more deeply than
those superficial layers. That is good advice, but at the same time, those
superficial layers of hair, skin, nails, etc. (known collectively as the
integument) have many interesting structures, and many important
biological functions. They protect organisms from many environmental
hazards and injuries, including disease, as well as heat or cold. To do this,
the integument relies on interactions with many other organ systems,
including the circulatory, nervous, and immune systems. Its beauty is
indeed more than skin-deep.
The Structure of Skin
Although you may not typically think of the skin as an organ, it is in fact
made of tissues that work together as a single structure to perform unique
and critical functions. The skin and its accessory structures make up the
integumentary system, which provides the body with overall protection.
The skin is made of multiple layers of cells and tissues, which are held to
underlying structures by connective tissue (Figure 1). The deeper layer of
skin is well vascularized (has numerous blood vessels). It also has
numerous sensory, and autonomic and sympathetic nerve fibers ensuring
communication to and from the brain. There are two main layers epidermis
and dermis with a third connective layer the hypodermis.
Layers of Skin
Hair shaft
Pore of sweat gland duct
Epidermis
|
|
Arrector pili
muscle
Hair follicle
Sebaceous (oil)
gland
Hypodermis
Hair root
Hair follicle
receptor Eccrine sweat gland
Pacinian corpuscle
Cutaneous vascular
plexus
Adipose tissue
Sensory nerve fiber
The skin is composed of two main layers: the epidermis,
made of closely packed epithelial cells, and the dermis,
made of dense, irregular connective tissue that houses
blood vessels, hair follicles, sweat glands, and other
structures. Beneath the dermis lies the hypodermis,
which is composed mainly of loose connective and fatty
tissues.
The Epidermis
The epidermis is composed of keratinized, stratified squamous epithelium.
It is made of four or five layers of epithelial cells, depending on its location
in the body. It does not have any blood vessels within it (i.e., it is
avascular). Skin that has four layers of cells is referred to as “thin skin.”
From deep to superficial, these layers are the stratum basale, stratum
spinosum, stratum granulosum, and stratum corneum. Most of the skin can
be classified as thin skin. “Thick skin” is found only on the palms of the
hands and the soles of the feet. It has a fifth layer, called the stratum
lucidum, located between the stratum corneum and the stratum granulosum
({link]).
Thin Skin versus Thick Skin
— fee oY
.
-
These slides show cross-
sections of the epidermis and
dermis of (a) thin and (b)
thick skin. Note the
significant difference in the
thickness of the epithelial
layer of the thick skin. From
top, LM x 40, LM ~x 40.
(Micrographs provided by the
Regents of University of
Michigan Medical School ©
2012)
The cells in all of the layers except the stratum basale are called
keratinocytes. A keratinocyte is a cell that manufactures and stores the
protein keratin. Keratin is an intracellular fibrous protein that gives hair,
nails, and skin their hardness and water-resistant properties. The
keratinocytes in the stratum corneum are dead and regularly slough away,
being replaced by cells from the deeper layers ({link]).
Epidermis
The epidermis is epithelium
composed of multiple layers
of cells. The basal layer
consists of cuboidal cells,
whereas the outer layers are
squamous, keratinized cells,
so the whole epithelium is
often described as being
keratinized stratified
squamous epithelium. LM x
40. (Micrograph provided by
the Regents of University of
Michigan Medical School ©
2012)
Layer of the Epidermis
Stratum basale
The stratum basale (also called the stratum germinativum) is the deepest
epidermal layer and attaches the epidermis to the basal lamina, below which
lie the layers of the dermis. The cells in the stratum basale bond to the
dermis via intertwining collagen fibers, referred to as the basement
membrane. A finger-like projection, or fold, known as the dermal papilla
(plural = dermal papillae) is found in the superficial portion of the dermis.
Dermal papillae increase the strength of the connection between the
epidermis and dermis; the greater the folding, the stronger the connections
made ((link]).Two other cell types are found dispersed among the basal
cells in the stratum basale. The first is a Merkel cell, which functions as a
receptor and is responsible for stimulating sensory nerves that the brain
perceives as touch. These cells are especially abundant on the surfaces of
the hands and feet. The second is a melanocyte, a cell that produces the
pigment melanin. Melanin gives hair and skin its color, and also helps
protect the living cells of the epidermis from ultraviolet (UV) radiation
damage.
Layers of the Epidermis
Dead cells filled
with keratin
Stratum corneum
Stratum lucidum ——_{_
Lamellar granules
— eae oun Ye S S
Ss - aa S—
Stratum spinosum g = = eae 6 HX Keratinocyte
2 a
ll < yz =
~ 2 “SS
if —_ Soe
Stratum basale = Y/,
> : Merkel cell
Ze)
Melanocyte
: Sensory neuron
Dermis
The epidermis of thick skin has five layers: stratum
basale, stratum spinosum, stratum granulosum, stratum
lucidum, and stratum corneum.
Stratum Spinosum
As the name suggests, the stratum spinosum is spiny in appearance due to
the protruding cell processes that join the cells via a structure called a
desmosome. The desmosomes interlock with each other and strengthen the
bond between the cells. It is interesting to note that the “spiny” nature of
this layer is an artifact of the staining process. Unstained epidermis samples
do not exhibit this characteristic appearance. The stratum spinosum is
composed of eight to 10 layers of keratinocytes, formed as a result of cell
division in the stratum basale ([link]). Interspersed among the keratinocytes
of this layer is a type of dendritic cell called the Langerhans cell, which
functions as a macrophage by engulfing bacteria, foreign particles, and
damaged cells that occur in this layer.
The keratinocytes in the stratum spinosum begin the synthesis of keratin
and release a water-repelling glycolipid that helps prevent water loss from
the body, making the skin relatively waterproof. As new keratinocytes are
produced atop the stratum basale, the keratinocytes of the stratum spinosum
are pushed into the stratum granulosum.
Stratum Granulosum
The stratum granulosum has a grainy appearance due to further changes
to the keratinocytes as they are pushed from the stratum spinosum. The
cells (three to five layers deep) become flatter, their cell membranes
thicken, and they generate large amounts of the proteins keratin, which is
fibrous, and keratohyalin, which accumulates as lamellar granules within
the cells (see [link]). These two proteins make up the bulk of the
keratinocyte mass in the stratum granulosum and give the layer its grainy
appearance. The nuclei and other cell organelles disintegrate as the cells
die, leaving behind the keratin, keratohyalin, and cell membranes that will
form the stratum lucidum, the stratum comeum, and the accessory
structures of hair and nails.
Stratum Lucidum
The stratum lucidum is a smooth, seemingly translucent layer of the
epidermis located just above the stratum granulosum and below the stratum
corneum. This thin layer of cells is found only in the thick skin of the
palms, soles, and digits. The keratinocytes that compose the stratum
lucidum are dead and flattened (see [link]). These cells are densely packed
with eleiden, a clear protein rich in lipids, derived from keratohyalin, which
gives these cells their transparent (i.e., lucid) appearance and provides a
barrier to water.
Stratum Corneum
The stratum corneum is the most superficial layer of the epidermis and is
the layer exposed to the outside environment (see [link]). The increased
keratinization (also called cornification) of the cells in this layer gives it its
name. There are usually 15 to 30 layers of cells in the stratum corneum.
This dry, dead layer helps prevent the penetration of microbes and the
dehydration of underlying tissues, and provides a mechanical protection
against abrasion for the more delicate, underlying layers. Cells in this layer
are shed periodically and are replaced by cells pushed up from the stratum
granulosum (or stratum lucidum in the case of the palms and soles of feet).
The entire layer is replaced during a period of about 4 weeks. Cosmetic
procedures, such as microdermabrasion, help remove some of the dry, upper
layer and aim to keep the skin looking “fresh” and healthy.
Dermis
The dermis might be considered the “core” of the integumentary system
(derma- = “skin”), as distinct from the epidermis (epi- = “upon” or “over”
and hypodermis (hypo- = “below”). It contains blood and lymph vessels,
nerves, and other structures, such as hair follicles and sweat glands. The
dermis is made of two layers of connective tissue that compose an
interconnected mesh of elastin and collagenous fibers, produced by
fibroblasts ({link]).
Layers of the Dermis
This stained slide shows the two
components of the dermis—the
papillary layer and the reticular
layer. Both are made of connective
tissue with fibers of collagen
extending from one to the other,
making the border between the
two somewhat indistinct. The
dermal papillae extending into the
epidermis belong to the papillary
layer, whereas the dense collagen
fiber bundles below belong to the
reticular layer. LM x 10. (credit:
modification of work by
“kilbad”/Wikimedia Commons)
Papillary Layer
The papillary layer is made of loose connective tissue, which means the
collagen and elastin fibers of this layer form a loose mesh. This superficial
layer of the dermis projects into the stratum basale of the epidermis to form
finger-like dermal papillae (see [link]). Within the papillary layer are
fibroblasts, a small number of fat cells (adipocytes), and an abundance of
small blood vessels. In addition, the papillary layer contains phagocytes,
defensive cells that help fight bacteria or other infections that have breached
the skin. This layer also contains lymphatic capillaries, nerve fibers, and
touch receptors called the Meissner corpuscles.
Reticular Layer
Underlying the papillary layer is the much thicker reticular layer,
composed of dense, irregular connective tissue. This layer is well
vascularized and has a rich sensory and sympathetic nerve supply. The
reticular layer appears reticulated (net-like) due to a tight meshwork of
fibers. Elastin fibers provide some elasticity to the skin, enabling
movement. Collagen fibers provide structure and tensile strength, with
strands of collagen extending into both the papillary layer and the
hypodermis. In addition, collagen binds water to keep the skin hydrated.
Collagen injections and Retin-A creams help restore skin turgor by either
introducing collagen externally or stimulating blood flow and repair of the
dermis, respectively.
Hypodermis
The hypodermis (also called the subcutaneous layer or superficial fascia) is
a layer directly below the dermis and serves to connect the skin to the
underlying fascia (fibrous tissue) of the bones and muscles. It is not strictly
a part of the skin, although the border between the hypodermis and dermis
can be difficult to distinguish. The hypodermis consists of well-
vascularized, loose, areolar connective tissue and adipose tissue, which
functions as a mode of fat storage and provides insulation and cushioning
for the integument.
Pigmentation
The color of skin is influenced by a number of pigments, including melanin,
carotene, and hemoglobin. Recall that melanin is produced by cells called
melanocytes, which are found scattered throughout the stratum basale of the
epidermis. The melanin is transferred into the keratinocytes via a cellular
vesicle called a melanosome ((link]).
Skin Pigmentation
Surface
Upper
keratinocytes
Melanosomes
Basal
keratinocytes
Melanocytes
The relative coloration of the skin depends of the amount of
melanin produced by melanocytes in the stratum basale and
taken up by keratinocytes.
Melanin occurs in two primary forms. Eumelanin exists as black and
brown, whereas pheomelanin provides a red color. Dark-skinned
individuals produce more melanin than those with pale skin. Exposure to
the UV rays of the sun or a tanning salon causes melanin to be
manufactured and built up in keratinocytes, as sun exposure stimulates
keratinocytes to secrete chemicals that stimulate melanocytes. The
accumulation of melanin in keratinocytes results in the darkening of the
skin, or a tan. This increased melanin accumulation protects the DNA of
epidermal cells from UV ray damage and the breakdown of folic acid, a
nutrient necessary for our health and well-being. In contrast, too much
melanin can interfere with the production of vitamin D, an important
nutrient involved in calcium absorption. Thus, the amount of melanin
present in our skin is dependent on a balance between available sunlight
and folic acid destruction, and protection from UV radiation and vitamin D
production.
It requires about 10 days after initial sun exposure for melanin synthesis to
peak, which is why pale-skinned individuals tend to suffer sunburns of the
epidermis initially. Dark-skinned individuals can also get sunburns, but are
more protected than are pale-skinned individuals. Melanosomes are
temporary structures that are eventually destroyed by fusion with
lysosomes; this fact, along with melanin-filled keratinocytes in the stratum
corneum sloughing off, makes tanning impermanent.
Too much sun exposure can eventually lead to wrinkling due to the
destruction of the cellular structure of the skin, and in severe cases, can
cause sufficient DNA damage to result in skin cancer. When there is an
irregular accumulation of melanocytes in the skin, freckles appear. Moles
are larger masses of melanocytes, and although most are benign, they
should be monitored for changes that might indicate the presence of cancer
({link]).
Moles
Moles range from benign accumulations
of melanocytes to melanomas. These
structures populate the landscape of our
skin. (credit: the National Cancer
Institute)
Accessory Structures of the Skin
Accessory structures of the skin include hair, nails, sweat glands, and
sebaceous glands. These structures embryologically originate from the
epidermis and can extend down through the dermis into the hypodermis.
Hair
Hair is a keratinous filament growing out of the epidermis. It is primarily
made of dead, keratinized cells. Strands of hair originate in an epidermal
penetration of the dermis called the hair follicle. The hair shaft is the part
of the hair not anchored to the follicle, and much of this is exposed at the
skin’s surface. The rest of the hair, which is anchored in the follicle, lies
below the surface of the skin and is referred to as the hair root. The hair
root ends deep in the dermis at the hair bulb, and includes a layer of
mitotically active basal cells called the hair matrix. The hair bulb
surrounds the hair papilla, which is made of connective tissue and contains
blood capillaries and nerve endings from the dermis ((Link]).
Hair
Medulla
Cortex
Cuticle
Sebaceous
gland
Inner root
sheath
Outer root
sheath
Hair matrix
Hair
papilla
Hair follicles originate in the
epidermis and have many
different parts.
Just as the basal layer of the epidermis forms the layers of epidermis that
get pushed to the surface as the dead skin on the surface sheds, the basal
cells of the hair bulb divide and push cells outward in the hair root and shaft
as the hair grows. The medulla forms the central core of the hair, which is
surrounded by the cortex, a layer of compressed, keratinized cells that is
covered by an outer layer of very hard, keratinized cells known as the
cuticle. These layers are depicted in a longitudinal cross-section of the hair
follicle ({link]), although not all hair has a medullary layer. Hair texture
(straight, curly) is determined by the shape and structure of the cortex, and
to the extent that it is present, the medulla. The shape and structure of these
layers are, in turn, determined by the shape of the hair follicle. Hair growth
begins with the production of keratinocytes by the basal cells of the hair
bulb. As new cells are deposited at the hair bulb, the hair shaft is pushed
through the follicle toward the surface. Keratinization is completed as the
cells are pushed to the skin surface to form the shaft of hair that is
externally visible. The external hair is completely dead and composed
entirely of keratin. For this reason, our hair does not have sensation.
Furthermore, you can cut your hair or shave without damaging the hair
structure because the cut is superficial. Most chemical hair removers also
act superficially; however, electrolysis and yanking both attempt to destroy
the hair bulb so hair cannot grow.
Hair Follicle
The slide shows a cross-section of a hair
follicle. Basal cells of the hair matrix in
the center differentiate into cells of the
inner root sheath. Basal cells at the base
of the hair root form the outer root sheath.
LM x 4. (credit: modification of work by
“kilbad”/Wikimedia Commons)
The wall of the hair follicle is made of three concentric layers of cells. The
cells of the internal root sheath surround the root of the growing hair and
extend just up to the hair shaft. They are derived from the basal cells of the
hair matrix. The external root sheath, which is an extension of the
epidermis, encloses the hair root. It is made of basal cells at the base of the
hair root and tends to be more keratinous in the upper regions. The glassy
membrane is a thick, clear connective tissue sheath covering the hair root,
connecting it to the tissue of the dermis.
Hair serves a variety of functions, including protection, sensory input,
thermoregulation, and communication. For example, hair on the head
protects the skull from the sun. The hair in the nose and ears, and around
the eyes (eyelashes) defends the body by trapping and excluding dust
particles that may contain allergens and microbes. Hair of the eyebrows
prevents sweat and other particles from dripping into and bothering the
eyes. Hair also has a sensory function due to sensory innervation by a hair
root plexus surrounding the base of each hair follicle. Hair is extremely
sensitive to air movement or other disturbances in the environment, much
more so than the skin surface. This feature is also useful for the detection of
the presence of insects or other potentially damaging substances on the skin
surface. Each hair root is connected to a smooth muscle called the arrector
pili that contracts in response to nerve signals from the sympathetic nervous
system, making the external hair shaft “stand up.” The primary purpose for
this is to trap a layer of air to add insulation. This is visible in humans as
goose bumps and even more obvious in animals, such as when a frightened
cat raises its fur. Of course, this is much more obvious in organisms with a
heavier coat than most humans, such as dogs and cats.
Hair Growth
Hair grows and is eventually shed and replaced by new hair. This occurs in
three phases. The first is the anagen phase, during which cells divide
rapidly at the root of the hair, pushing the hair shaft up and out. The length
of this phase is measured in years, typically from 2 to 7 years. The catagen
phase lasts only 2 to 3 weeks, and marks a transition from the hair follicle’s
active growth. Finally, during the telogen phase, the hair follicle is at rest
and no new growth occurs. At the end of this phase, which lasts about 2 to 4
months, another anagen phase begins. The basal cells in the hair matrix then
produce a new hair follicle, which pushes the old hair out as the growth
cycle repeats itself. Hair typically grows at the rate of 0.3 mm per day
during the anagen phase. On average, 50 hairs are lost and replaced per day.
Hair loss occurs if there is more hair shed than what is replaced and can
happen due to hormonal or dietary changes. Hair loss can also result from
the aging process, or the influence of hormones.
Hair Color
Similar to the skin, hair gets its color from the pigment melanin, produced
by melanocytes in the hair papilla. Different hair color results from
differences in the type of melanin, which is genetically determined. As a
person ages, the melanin production decreases, and hair tends to lose its
color and becomes gray and/or white.
Nails
The nail bed is a specialized structure of the epidermis that is found at the
tips of our fingers and toes. The nail body is formed on the nail bed, and
protects the tips of our fingers and toes as they are the farthest extremities
and the parts of the body that experience the maximum mechanical stress
({link]). In addition, the nail body forms a back-support for picking up
small objects with the fingers. The nail body is composed of densely packed
dead keratinocytes. The epidermis in this part of the body has evolved a
specialized structure upon which nails can form. The nail body forms at the
nail root, which has a matrix of proliferating cells from the stratum basale
that enables the nail to grow continuously. The lateral nail fold overlaps the
nail on the sides, helping to anchor the nail body. The nail fold that meets
the proximal end of the nail body forms the nail cuticle, also called the
eponychium. The nail bed is rich in blood vessels, making it appear pink,
except at the base, where a thick layer of epithelium over the nail matrix
forms a crescent-shaped region called the lunula (the “little moon”). The
area beneath the free edge of the nail, furthest from the cuticle, is called the
hyponychium. It consists of a thickened layer of stratum corneum.
Nails
Free edge Eponychium
OES. Proximal nail fold Lunula
Nail vA 2
Nail body
Lateral nail fold
Lunula
Eponychium
Proximal nail fold
Epidermis Dermis Phalanx Hyponychium
The nail is an accessory structure of the integumentary
system.
Sweat Glands
When the body becomes warm, sudoriferous glands produce sweat to cool
the body. Sweat glands develop from epidermal projections into the dermis
and are classified as merocrine glands; that is, the secretions are excreted by
exocytosis through a duct without affecting the cells of the gland. There are
two types of sweat glands, each secreting slightly different products.
An eccrine sweat gland is type of gland that produces a hypotonic sweat
for thermoregulation. These glands are found all over the skin’s surface, but
are especially abundant on the palms of the hand, the soles of the feet, and
the forehead ([link]). They are coiled glands lying deep in the dermis, with
the duct rising up to a pore on the skin surface, where the sweat is released.
This type of sweat, released by exocytosis, is hypotonic and composed
mostly of water, with some salt, antibodies, traces of metabolic waste, and
dermicidin, an antimicrobial peptide. Eccrine glands are a primary
component of thermoregulation in humans and thus help to maintain
homeostasis.
Eccrine Gland
Skin surface
Eccrine sweat
gland
Eccrine glands are coiled glands in the
dermis that release sweat that is
mostly water.
An apocrine sweat gland is usually associated with hair follicles in densely
hairy areas, such as armpits and genital regions. Apocrine sweat glands are
larger than eccrine sweat glands and lie deeper in the dermis, sometimes
even reaching the hypodermis, with the duct normally emptying into the
hair follicle. In addition to water and salts, apocrine sweat includes organic
compounds that make the sweat thicker and subject to bacterial
decomposition and subsequent smell. The release of this sweat is under
both nervous and hormonal control, and plays a role in the poorly
understood human pheromone response. Most commercial antiperspirants
use an aluminum-based compound as their primary active ingredient to stop
sweat. When the antiperspirant enters the sweat gland duct, the aluminum-
based compounds precipitate due to a change in pH and form a physical
block in the duct, which prevents sweat from coming out of the pore.
Sebaceous Glands
A sebaceous gland is a type of oil gland that is found all over the body and
helps to lubricate and waterproof the skin and hair. Most sebaceous glands
are associated with hair follicles. They generate and excrete sebum, a
mixture of lipids, onto the skin surface, thereby naturally lubricating the dry
and dead layer of keratinized cells of the stratum corneum, keeping it
pliable. The fatty acids of sebum also have antibacterial properties, and
prevent water loss from the skin in low-humidity environments. The
secretion of sebum is stimulated by hormones, many of which do not
become active until puberty. Thus, sebaceous glands are relatively inactive
during childhood.
Functions of the Skin
The skin and accessory structures perform a variety of essential functions,
such as protecting the body from invasion by microorganisms, chemicals,
and other environmental factors; preventing dehydration; acting as a
sensory organ; modulating body temperature and electrolyte balance; and
synthesizing vitamin D. The underlying hypodermis has important roles in
storing fats, forming a “cushion” over underlying structures, and providing
insulation from cold temperatures.
Protection
The skin protects the rest of the body from the basic elements of nature
such as wind, water, and UV sunlight. It acts as a protective barrier against
water loss, due to the presence of layers of keratin and glycolipids in the
stratum corneum. It also is the first line of defense against abrasive activity
due to contact with grit, microbes, or harmful chemicals. Sweat excreted
from sweat glands deters microbes from over-colonizing the skin surface by
generating dermicidin, which has antibiotic properties.
Sensory Function
The fact that you can feel an ant crawling on your skin, allowing you to
flick it off before it bites, is because the skin, and especially the hairs
projecting from hair follicles in the skin, can sense changes in the
environment. The hair root plexus surrounding the base of the hair follicle
senses a disturbance, and then transmits the information to the central
nervous system (brain and spinal cord), which can then respond by
activating the skeletal muscles of your eyes to see the ant and the skeletal
muscles of the body to act against the ant.
The skin acts as a sense organ because the epidermis, dermis, and the
hypodermis contain specialized sensory nerve structures that detect touch,
surface temperature, and pain. These receptors are more concentrated on the
tips of the fingers, which are most sensitive to touch, especially the
Meissner corpuscle (tactile corpuscle) ([link]), which responds to light
touch, and the Pacinian corpuscle (lamellated corpuscle), which responds
to vibration. Merkel cells, seen scattered in the stratum basale, are also
touch receptors. In addition to these specialized receptors, there are sensory
nerves connected to each hair follicle, pain and temperature receptors
scattered throughout the skin, and motor nerves innervate the arrector pili
muscles and glands. This rich innervation helps us sense our environment
and react accordingly.
Light Micrograph of a Meissner Corpuscle
In this micrograph of a skin cross-section,
you can see a Meissner corpuscle (arrow),
a type of touch receptor located in a
dermal papilla adjacent to the basement
membrane and stratum basale of the
overlying epidermis. LM x 100. (credit:
“Wbensmith”/Wikimedia Commons)
Thermoregulation
The integumentary system helps regulate body temperature through its tight
association with the sympathetic nervous system, the division of the
nervous system involved in our fight-or-flight responses. The sympathetic
nervous system is continuously monitoring body temperature and initiating
appropriate motor responses. Recall that sweat glands, accessory structures
to the skin, secrete water, salt, and other substances to cool the body when it
becomes warm. Even when the body does not appear to be noticeably
sweating, approximately 500 mL of sweat (insensible perspiration) are
secreted a day. If the body becomes excessively warm due to high
temperatures, vigorous activity ((link]ac), or a combination of the two,
sweat glands will be stimulated by the sympathetic nervous system to
produce large amounts of sweat, as much as 0.7 to 1.5 L per hour for an
active person. When the sweat evaporates from the skin surface, the body is
cooled as body heat is dissipated.
In addition to sweating, arterioles in the dermis dilate so that excess heat
carried by the blood can dissipate through the skin and into the surrounding
environment ({link]b). This accounts for the skin redness that many people
experience when exercising.
Thermoregulation
Heat is retained Heat through .
by your body radiation and convection ae
Heat loss
—— Skin surface
\ Blood circulates
___\\\.__- to surface of
skin to dispel
heat
Blood circulation
avoids surface
-— of skin to retain yo
(a) (b)
During strenuous physical activities, such as skiing (a) or
running (c), the dermal blood vessels dilate and sweat secretion
increases (b). These mechanisms prevent the body from
overheating. In contrast, the dermal blood vessels constrict to
minimize heat loss in response to low temperatures (b). (credit
a: “Trysil”/flickr; credit c: Ralph Daily)
When body temperatures drop, the arterioles constrict to minimize heat
loss, particularly in the ends of the digits and tip of the nose. This reduced
circulation can result in the skin taking on a whitish hue. Although the
temperature of the skin drops as a result, passive heat loss is prevented, and
internal organs and structures remain warm. If the temperature of the skin
drops too much (such as environmental temperatures below freezing), the
conservation of body core heat can result in the skin actually freezing, a
condition called frostbite.
Note:
Aging and the...
Integumentary System
All systems in the body accumulate subtle and some not-so-subtle changes
as a person ages. Among these changes are reductions in cell division,
metabolic activity, blood circulation, hormonal levels, and muscle strength
({link]). In the skin, these changes are reflected in decreased mitosis in the
stratum basale, leading to a thinner epidermis. The dermis, which is
responsible for the elasticity and resilience of the skin, exhibits a reduced
ability to regenerate, which leads to slower wound healing. The
hypodermis, with its fat stores, loses structure due to the reduction and
redistribution of fat, which in turn contributes to the thinning and sagging
of skin.
Aging
Generally, skin, especially on the face and
hands, starts to display the first noticeable
signs of aging, as it loses its elasticity
over time. (credit: Janet Ramsden)
The accessory structures also have lowered activity, generating thinner hair
and nails, and reduced amounts of sebum and sweat. A reduced sweating
ability can cause some elderly to be intolerant to extreme heat. Other cells
in the skin, such as melanocytes and dendritic cells, also become less
active, leading to a paler skin tone and lowered immunity. Wrinkling of the
skin occurs due to breakdown of its structure, which results from decreased
collagen and elastin production in the dermis, weakening of muscles lying
under the skin, and the inability of the skin to retain adequate moisture.
Many anti-aging products can be found in stores today. In general, these
products try to rehydrate the skin and thereby fill out the wrinkles, and
some stimulate skin growth using hormones and growth factors.
Additionally, invasive techniques include collagen injections to plump the
tissue and injections of BOTOX® (the name brand of the botulinum
neurotoxin) that paralyze the muscles that crease the skin and cause
wrinkling.
Vitamin D Synthesis
The epidermal layer of human skin synthesizes vitamin D when exposed to
UV radiation. In the presence of sunlight, a form of vitamin D3 called
cholecalciferol is synthesized from a derivative of the steroid cholesterol in
the skin. The liver converts cholecalciferol to calcidiol, which is then
converted to calcitriol (the active chemical form of the vitamin) in the
kidneys. Vitamin D is essential for normal absorption of calcium and
phosphorous, which are required for healthy bones. The absence of sun
exposure can lead to a lack of vitamin D in the body, leading to a condition
called rickets, a painful condition in children where the bones are
misshapen due to a lack of calcium, causing bowleggedness. Elderly
individuals who suffer from vitamin D deficiency can develop a condition
called osteomalacia, a softening of the bones. In present day society,
vitamin D is added as a supplement to many foods, including milk and
orange juice, compensating for the need for sun exposure.
In addition to its essential role in bone health, vitamin D is essential for
general immunity against bacterial, viral, and fungal infections. Recent
studies are also finding a link between insufficient vitamin D and cancer.
Sensory Systems
Introduction
" The act of smelling something, anything, is remarkably like the act of
thinking. Immediately at the moment of perception, you can feel the mind
going to work, sending the odor around from place to place, setting off
complex repertories through the brain, polling one center after another for
signs of recognition, for old memories and old connection." Lewis Thomas,
On Smell, 1985
Senses provide information about the body and its environment. Humans
have five special senses: olfaction (smell), gustation (taste), equilibrium
(balance and body position), vision, and hearing. Additionally, we possess
general senses, also called somatosensation, which respond to stimuli like
temperature, pain, pressure, and vibration. Vestibular sensation, which is an
organism’s sense of spatial orientation and balance, proprioception (position
of bones, joints, and muscles), and the sense of limb position that is used to
track kinesthesia (limb movement) are part of somatosensation. Although
the sensory systems associated with these senses are very different, all share
a common function: to convert a stimulus (such as light, or sound, or the
position of the body) into an electrical signal in the nervous system. This
process is called sensory transduction. We are going to focus on the five
special senses of humans.
There are three types of stimuli that are detected by the human sensory
systems. The first is chemical stimulus, where molecules stimulate a
sensory neuron. Chemical stimuli are detected by the olfactory system,
when molecules in the air bind to sensory cells in the nasal epithelia, and in
the gustation (taste) system, when molecules in your food stimulate your
taste buds. The second is electromagnetic radiation; light interacts with
molecules in the sensory cells (rods and cones) of your retina, and those
sensory cells send a signal to your brain. The third is mechanical
stimulation, where the sensory cells are activated by movement or touch.
Mechanical stimuli are detected by the cells in the inner ear that help you
detect balance and body position, and by other cells in your inner ear detect
sound (the sense of hearing). Additionally, mechanical stimuli are involved
in other somatosensory systems, such as pressure, pain, or vibration, in
proprioception (position of legs, arms and other body parts), and in
kinesthesia (detection of motion of those same body parts.
Sensory Perception
Reception
The first step in sensation is reception, which is the activation of sensory
receptors by stimuli such as mechanical stimuli (being bent or squished, for
example), chemicals, or temperature. The receptor can then respond to the
stimuli. The region in space in which a given sensory receptor can respond
to a stimulus, be it far away or in contact with the body, is that receptor’s
receptive field. Think for a moment about the differences in receptive fields
for the different senses. For the sense of touch, a stimulus must come into
contact with body. For the sense of hearing, a stimulus can be a moderate
distance away (some baleen whale sounds can propagate for many
kilometers). For vision, a stimulus can be very far away; for example, the
visual system perceives light from stars at enormous distances.
Transduction
The most fundamental function of a sensory system is the translation of a
sensory signal to an electrical signal in the nervous system. This takes place
at the sensory receptor, and a produces a change in electrical potential in
response to the stimulus. This is called the receptor potential. How is
sensory input, such as pressure on the skin, changed to a receptor potential?
In one example, a type of receptor called a mechanoreceptor (as shown in
[link]) possesses specialized membranes that respond to pressure.
Disturbance of these dendrites by compressing them or bending them opens
gated ion channels in the plasma membrane of the sensory neuron,
changing its electrical potential. Recall that in the nervous system, a
positive change of a neuron’s electrical potential (also called the membrane
potential), depolarizes the neuron. Receptor potentials are graded potentials:
the magnitude of these graded (receptor) potentials varies with the strength
of the stimulus. If the magnitude of depolarization is sufficient (that is, if
membrane potential reaches a threshold), the neuron will fire an action
potential. In all cases the appropriate stimulus will cause a change in the
membrane potential of the sensory cell; the exact mechanism for changing
the membrane potential will be different for different sensory calls.
Tectorial membrane
Plasma
membrane
> Outer hair cells
Tectorial membrane
Stereocillia
Deflected
aaa ae UU |
Cytoskeleton
Basilar membrane Cochlear nerve Inner hair cell
(a) (b)
(a) Mechanosensitive ion channels are gated ion channels that
respond to mechanical deformation of the plasma membrane. A
mechanosensitive channel is connected to the plasma
membrane and the cytoskeleton by hair-like tethers. When
pressure causes the extracellular matrix to move, the channel
opens, allowing ions to enter or exit the cell. (b) Stereocilia in
the human ear are connected to mechanosensitive ion channels.
When a sound causes the stereocilia to move,
mechanosensitive ion channels transduce the signal to the
cochlear nerve.
Sensory receptors for different senses are very different from each other,
and they are specialized according to the type of stimulus they sense: they
have receptor specificity. For example, touch receptors, light receptors, and
sound receptors are each activated by different stimuli. Touch receptors are
not sensitive to light or sound; they are sensitive only to touch or pressure.
However, stimuli may be combined at higher levels in the brain, as happens
with olfaction, contributing to our sense of taste.
Perception
Perception is an individual’s interpretation of a sensation. Although
perception relies on the activation of sensory receptors, perception happens
not at the level of the sensory receptor, but at higher levels in the nervous
system, in the brain. The brain distinguishes sensory stimuli through a
sensory pathway: action potentials from sensory receptors travel along
neurons that are dedicated to a particular stimulus. These neurons are
dedicated to that particular stimulus and synapse with particular neurons in
the brain or spinal cord.
All sensory signals, except those from the olfactory system, are transmitted
though the central nervous system and are routed to the thalamus and to the
appropriate region of the cortex. Recall that the thalamus is a structure in
the forebrain that serves as a clearinghouse and relay station for sensory (as
well as motor) signals. When the sensory signal exits the thalamus, it is
conducted to the specific area of the cortex ([link]) dedicated to processing
that particular sense.
How are neural signals interpreted? Interpretation of sensory signals
between individuals of the same species is largely similar, owing to the
inherited similarity of their nervous systems; however, there are some
individual differences. A good example of this is individual tolerances to a
painful stimulus, such as dental pain, which certainly differ. Interestingly,
studies have shown that the allele that results in red hair in humans
homozygous for that allele (known as MC1R) is a member of the family of
sensory receptors that detect pain. And redheads are more sensitive to pain,
and require about 20% more anesthetic during surgery or dental work. So
be nice to your red-headed friends.
Somatosensory
“processing region
Auditory processing Visual processing
region region
(a) (b)
In humans, with the exception of olfaction, all sensory
signals are routed from the (a) thalamus to (b) final
processing regions in the cortex of the brain. (credit b:
modification of work by Polina Tishina)
Taste and Smell
Taste, also called gustation, and smell, also called olfaction, are the most
interconnected senses in that both involve molecules of the stimulus
entering the body and bonding to receptors. Smell lets an animal sense the
presence of food or other animals—whether potential mates, predators, or
prey—or other chemicals in the environment that can impact their survival.
Similarly, the sense of taste allows animals to discriminate between types of
foods. While the value of a sense of smell is obvious, what is the value of a
sense of taste? Different tasting foods have different attributes, both helpful
and harmful. For example, sweet-tasting substances tend to be highly
caloric, which could be necessary for survival in lean times. Bitterness is
associated with toxicity, and sourness is associated with spoiled food. Salty
foods are valuable in maintaining homeostasis by helping the body retain
water and by providing ions necessary for cells to function.
Tastes and Odors
Both taste and odor stimuli are molecules taken in from the environment.
The primary tastes detected by humans are sweet, sour, bitter, salty and
umami. The first four tastes need little explanation. The identification of
umami as a fundamental taste occurred fairly recently—it was identified in
1908 by Japanese scientist Kikunae Ikeda while he worked with seaweed
broth, but it was not widely accepted as a taste that could be physiologically
distinguished until many years later. The taste of umami, also known as
savoriness, is attributable to the taste of the amino acid L-glutamate. In fact,
monosodium glutamate, or MSG, is often used in cooking to enhance the
savory taste of certain foods. What is the adaptive value of being able to
distinguish umami? Savory substances tend to be high in protein.
All odors that we perceive are volatile chemicals in the air we breathe. If a
substance does not release molecules into the air from its surface, it has no
smell. And if a human or other animal does not have a receptor that
recognizes a specific molecule, then that molecule has no smell. Humans
have about 350 olfactory receptor subtypes that work in various
combinations to allow us to sense about 10,000 different odors. Compare
that to mice, for example, which have about 1,300 olfactory receptor types,
and therefore probably sense more odors. Both odors and tastes involve
molecules that stimulate specific chemoreceptors. Although humans
commonly distinguish taste as one sense and smell as another, they work
together to create the perception of flavor. A person’s perception of flavor is
reduced if he or she has congested nasal passages.
Reception and Transduction
Taste
Detecting a taste (gustation) is fairly similar to detecting an odor
(olfaction), given that both taste and smell rely on chemical receptors being
stimulated by certain molecules. The primary organ of taste is the taste bud.
A taste bud is a cluster of gustatory receptors (taste cells) that are located
within the bumps on the tongue called papillae (singular: papilla)
(illustrated in [link]).
Circumvallate papillae
Foliate
papillae Fungiform papillae
Filiform papillae
(a) Foliate, circumvallate, and fungiform papillae are
located on different regions of the tongue. (b) Foliate
papillae are prominent protrusions on this light micrograph.
(credit a: modification of work by NCI; scale-bar data from
Matt Russell)
Each taste bud’s taste cells are replaced every 10 to 14 days. These are
elongated cells with hair-like processes called microvilli at the tips that
extend into the taste bud pore (illustrate in [link]). Food molecules (tastants)
are dissolved in saliva, and they bind with and stimulate the receptors on
the microvilli. The receptors for tastants are located across the outer portion
and front of the tongue, outside of the middle area where the filiform
papillae are most prominent.
Oral Cavity Microvilli Taste pore
ee
“> Epidermis of tongue
\- Supporting
mm cell
yp
Pores in the tongue allow tastants to enter taste
pores in the tongue. (credit: modification of
work by Vincenzo Rizzo)
In humans, there are five primary tastes, and each taste has only one
corresponding type of receptor. Thus, like olfaction, each receptor is
specific to its stimulus (tastant). Both tasting abilities and sense of smell
change with age. In humans, the senses decline dramatically by age 50 and
continue to decline. A child may find a food to be too spicy, whereas an
elderly person may find the same food to be bland and unappetizing.
Hearing and Equilibrium
Audition, or hearing, is important to humans and to other animals for many
different interactions. It enables an organism to detect and receive
information about danger, such as an approaching predator, and to
participate in communal exchanges like those concerning territories or
mating. On the other hand, although it is physically linked to the auditory
system, the vestibular system is not involved in hearing. Instead, an
animal’s vestibular system detects its own movement, both linear and
angular acceleration and deceleration, and balance.
Sound
Auditory stimuli are sound waves, which are mechanical, pressure waves
that move through a medium, such as air or water. There are no sound
waves in a vacuum since there are no air molecules to move in waves. The
speed of sound waves differs, based on altitude, temperature, and medium,
but at sea level and a temperature of 20° C (68° F), sound waves travel in
the air at about 343 meters per second.
As is true for all waves, there are four main characteristics of a sound wave:
frequency, wavelength, period, and amplitude. Frequency is the number of
waves per unit of time, and in sound is heard as pitch. High-frequency
(>15.000Hz) sounds are higher-pitched (short wavelength) than low-
frequency (long wavelengths; <100Hz) sounds. Frequency is measured in
cycles per second, and for sound, the most commonly used unit is hertz
(Hz), or cycles per second. Most humans can perceive sounds with
frequencies between 30 and 20,000 Hz. Women are typically better at
hearing high frequencies, but everyone’s ability to hear high frequencies
decreases with age. Dogs detect up to about 40,000 Hz; cats, 60,000 Hz;
bats, 100,000 Hz; and dolphins 150,000 Hz, and American shad (Alosa
sapidissima), a fish, can hear 180,000 Hz. Those frequencies above the
human range are called ultrasound.
Reception of Sound
In mammals, sound waves are collected by the external, cartilaginous part
of the ear called the pinna, then travel through the auditory canal and cause
vibration of the thin diaphragm called the tympanum or ear drum, the
innermost part of the outer ear (illustrated in [link]). Interior to the
tympanum is the middle ear. The middle ear holds three small bones called
the ossicles, which transfer energy from the moving tympanum to the inner
ear. The three ossicles are the malleus (also known as the hammer), the
incus (the anvil), and stapes (the stirrup). The aptly named stapes looks very
much like a stirrup. The three ossicles are unique to mammals, and each
plays a role in hearing. The malleus attaches at three points to the interior
surface of the tympanic membrane. The incus attaches the malleus to the
stapes. In humans, the stapes is not long enough to reach the tympanum. If
we did not have the malleus and the incus, then the vibrations of the
tympanum would never reach the inner ear. These bones also function to
collect force and amplify sounds. The ear ossicles are homologous to bones
in a fish mouth: the bones that support gills in fish are thought to have been
adapted for use in the vertebrate ear over evolutionary time.
Stapes
(attached to oval window)
Semicircular
Malleus
Vestibular nerve
Cochlear
nerve
Cochlea
Ear canal ;
Tympanic
cavity
Tympanum Eustachian tube
Round window
Sound travels through the outer ear to the middle ear, which
is bounded on its exterior by the tympanic membrane. The
middle ear contains three bones called ossicles that transfer
the sound wave to the oval window, the exterior boundary
of the inner ear. The organ of Corti, which is the organ of
sound transduction, lies inside the cochlea. (credit:
modification of work by Lars Chittka, Axel Brockmann)
Vestibular Information
The stimuli associated with the vestibular system are linear acceleration
(gravity) and angular acceleration and deceleration. Gravity, acceleration,
and deceleration are detected by evaluating the inertia on receptive cells in
the vestibular system. Gravity is detected through head position. Angular
acceleration and deceleration are expressed through turning or tilting of the
head.
The vestibular system has some similarities with the auditory system. It
utilizes hair cells just like the auditory system, but it excites them in
different ways. There are five vestibular receptor organs in the inner ear: the
utricle, the saccule, and three semicircular canals. Together, they make up
what’s known as the vestibular labyrinth that is shown in [link]. The utricle
and saccule respond to acceleration in a straight line, such as gravity. The
roughly 30,000 hair cells in the utricle and 16,000 hair cells in the saccule
lie below a gelatinous layer, with their stereocilia projecting into the gelatin.
Embedded in this gelatin are calcium carbonate crystals—like tiny rocks.
When the head is tilted, the crystals continue to be pulled straight down by
gravity, but the new angle of the head causes the gelatin to shift, thereby
bending the stereocilia. The bending of the stereocilia stimulates the
neurons, and they signal to the brain that the head is tilted, allowing the
maintenance of balance. It is the vestibular branch of the vestibulocochlear
cranial nerve that deals with balance.
Posterior Canal
Superior Canal
Urticle
=o
a , Cochlea
vy
es, \
Horizontal
Canal
Vestibule
Saccule
The structure of the vestibular
labyrinth is shown. (credit:
modification of work by NIH)
The fluid-filled semicircular canals are tubular loops set at oblique angles.
They are arranged in three spatial planes. The base of each canal has a
swelling that contains a cluster of hair cells. The hairs project into a
gelatinous cap called the cupula and monitor angular acceleration and
deceleration from rotation. They would be stimulated by driving your car
around a corner, turning your head, or falling forward. One canal lies
horizontally, while the other two lie at about 45 degree angles to the
horizontal axis, as illustrated in [link]. When the brain processes input from
all three canals together, it can detect angular acceleration or deceleration in
three dimensions. When the head turns, the fluid in the canals shifts,
thereby bending stereocilia and sending signals to the brain. Upon cessation
accelerating or decelerating—or just moving—the movement of the fluid
within the canals slows or stops. For example, imagine holding a glass of
water. When moving forward, water may splash backwards onto the hand,
and when motion has stopped, water may splash forward onto the fingers.
While in motion, the water settles in the glass and does not splash. Note that
the canals are not sensitive to velocity itself, but to changes in velocity, so
moving forward at 6(0mph with your eyes closed would not give the
sensation of movement, but suddenly accelerating or braking would
stimulate the receptors.
Vision
Vision is the ability to detect light patterns from the outside environment
and interpret them into images. Animals are bombarded with sensory
information, and the sheer volume of visual information can be
problematic. Fortunately, the visual systems of species have evolved to
attend to the most-important stimuli. The importance of vision to humans is
further substantiated by the fact that about one-third of the human cerebral
cortex is dedicated to analyzing and perceiving visual information.
Light
As with auditory stimuli, light travels in waves. The compression waves
that compose sound must travel in a medium—a gas, a liquid, or a solid. In
contrast, light is composed of electromagnetic waves and needs no medium;
light can travel in a vacuum ((link]). The behavior of light can be discussed
in terms of the behavior of waves and also in terms of the behavior of the
fundamental unit of light—a packet of electromagnetic radiation called a
photon. A glance at the electromagnetic spectrum shows that visible light
for humans is just a small slice of the entire spectrum, which includes
radiation that we cannot see as light because it is below the frequency of
visible red light and above the frequency of visible violet light.
Certain variables are important when discussing perception of light.
Wavelength (which varies inversely with frequency) manifests itself as hue.
Light at the red end of the visible spectrum has longer wavelengths (and is
lower frequency), while light at the violet end has shorter wavelengths (and
is higher frequency). The wavelength of light is expressed in nanometers
(nm); one nanometer is one billionth of a meter. Humans perceive light that
ranges between approximately 380 nm and 740 nm. Some other animals,
though, can detect wavelengths outside of the human range. For example,
bees see near-ultraviolet light in order to locate nectar guides on flowers,
and some non-avian reptiles sense infrared light (heat that prey gives off).
Wavelength
(meters) Radio Microwave Infrared Visible Ultraviolet X-ray Gamma ray
10° 10? 10° 5x 10° 10° 107° 10
line a x ee @
Buildings Humans Honeybee Pinpoint Protozoans Molecules Atoms Atomic nuclei
I SSS
(Hz)
10* 108 10% 10% 10** 108 10”
In the electromagnetic spectrum, visible light lies between
380 nm and 740 nm. (credit: modification of work by
NASA)
Wave amplitude is perceived as luminous intensity, or brightness. The
standard unit of intensity of light is the candela, which is approximately the
luminous intensity of a one common candle.
Light waves travel 299,792 km per second in a vacuum, (and somewhat
slower in various media such as air and water), and those waves atrive at
the eye as long (red), medium (green), and short (blue) waves. What is
termed “white light” is light that is perceived as white by the human eye.
This effect is produced by light that stimulates equally the color receptors in
the human eye. The apparent color of an object is the color (or colors) that
the object reflects. Thus a red object reflects the red wavelengths in mixed
(white) light and absorbs all other wavelengths of light.
Anatomy of the Eye
The photoreceptive cells of the eye, where transduction of light to nervous
impulses occurs, are located in the retina (shown in [link]) on the inner
surface of the back of the eye. But light does not impinge on the retina
unaltered. It passes through other layers that process it so that it can be
interpreted by the retina ([link]b). The cornea, the front transparent layer of
the eye, and the crystalline lens, a transparent convex structure behind the
comea, both refract (bend) light to focus the image on the retina. The iris,
which is conspicuous as the colored part of the eye, is a circular muscular
ring lying between the lens and cornea that regulates the amount of light
entering the eye. In conditions of high ambient light, the iris contracts,
reducing the size of the pupil at its center. In conditions of low light, the iris
relaxes and the pupil enlarges.
Optic nerve
Light
Cornea
._— Aqueous humour wy > wy > ~s
Retina
Ganglion
cells
Vitreous /
humour bs Amacrine
y cells
Bipolar cells
Horizontal
cells
Optic nerve
Fovea | =— Cone
Retinal
blood vessels
(a) The human eye is shown in cross section. (b) A blowup
shows the layers of the retina.
The main function of the lens is to focus light on the retina and fovea
centralis. The lens is dynamic, focusing and re-focusing light as the eye
rests on near and far objects in the visual field. The lens is operated by
muscles that stretch it flat or allow it to thicken, changing the focal length
of light coming through it to focus it sharply on the retina. With age comes
the loss of the flexibility of the lens, and a form of farsightedness called
presbyopia results. Presbyopia occurs because the image focuses behind the
retina. Presbyopia is a deficit similar to a different type of farsightedness
called hyperopia caused by an eyeball that is too short. For both defects,
images in the distance are clear but images nearby are blurry. Myopia
(nearsightedness) occurs when an eyeball is elongated and the image focus
falls in front of the retina. In this case, images in the distance are blurry but
images nearby are clear.
There are two types of photoreceptors in the retina: rods and cones, named
for their general appearance as illustrated in [link]. Rods are strongly
photosensitive and are located in the outer edges of the retina. They detect
dim light and are used primarily for peripheral and nighttime vision. Cones
are weakly photosensitive and are located near the center of the retina. They
respond to bright light, and their primary role is in daytime, color vision.
Outer segment
contains rhodopsin
Rod outer
segment
Outer segment
contains
photopigments
Oil droplet
Nucleus
Rods and cones are photoreceptors
in the retina. Rods respond in low
light and can detect only shades of
gray. Cones respond in intense
light and are responsible for color
vision. (credit: modification of
work by Piotr Sliwa)
The fovea is the region in the center back of the eye that is responsible for
acute vision. The fovea has a high density of cones. When you bring your
gaze to an object to examine it intently in bright light, the eyes orient so that
the object’s image falls on the fovea. However, when looking at a star in the
night sky or other object in dim light, the object can be better viewed by the
peripheral vision because it is the rods at the edges of the retina, rather than
the cones at the center, that operate better in low light. In humans, cones far
outnumber rods in the fovea.
Transduction of Light
The rods and cones are the site of transduction of light to a neural signal.
Both rods and cones contain photopigments. In vertebrates, the main
photopigment, rhodopsin, has two main parts: an opsin, which is a
membrane protein (in the form of a cluster of a-helices that span the
membrane), and retinal—a molecule that absorbs light. When light hits a
photoreceptor, it causes a shape change in the retinal, altering its structure
from a bent (cis) form of the molecule to its linear (trans) isomer. This
isomerization of retinal activates the rhodopsin, starting a cascade of events
that ends with a change in the membrane potential of the rod or cone cell.
Trichromatic Coding
There are three types of cones (with different photopsins), and they differ in
the wavelength to which they are most responsive, as shown in [link]. Some
cones are maximally responsive to short light waves of 420 nm, so they are
called S cones (“S” for “short”); others respond maximally to waves of 530
nm (M cones, for “medium”); a third group responds maximally to light of
longer wavelengths, at 560 nm (L, or “long” cones). With only one type of
cone, color vision would not be possible, and a two-cone (dichromatic)
system has limitations. Primates use a three-cone (trichromatic) system,
resulting in full color vision.
The color we perceive is a result of the ratio of activity of our three types of
cones. The colors of the visual spectrum, running from long-wavelength
light to short, are red (700 nm), orange (600 nm), yellow (565 nm), green
(497 nm), blue (470 nm), indigo (450 nm), and violet (425 nm). Humans
have very sensitive perception of color and can distinguish about 500 levels
of brightness, 200 different hues, and 20 steps of saturation, or about 2
million distinct colors.
Normalized absorbance
400 500 600 700
Wavelength (nm)
Human rod cells and the different types of
cone cells each have an optimal
wavelength. However, there is
considerable overlap in the wavelengths
of light detected.
Reflexes and Homeostasis
Introduction
"There is no other species on Earth that does science. It is, so far, entirely a
human invention, evolved by natural selection in the human cortex for one
simple reason: it works. It is not perfect. It is misused. It is only a tool. But
it is by far the best tool we have, self-correcting, ongoing, applicable to
everything.” Carl Sagan, American astronomer, in Cosmos, 1980
As we come to the last section of this book, it seems appropriate to hearken
back to where we started - with a reminder that science is a way of
knowing. The knowledge of animal biology discussed in this module, and
the mechanisms of nervous system function, homeostasis, etc. are all
products of painstaking experiments and observations, in some cases dating
back hundreds of years. This uniquely human endeavor gave us that
knowledge. More importantly, animal biology is just a subset of the science
of biology, and biology is just a subset of science. There is a lot more to
explore in other areas of science, and infinitely more for current and future
humans to learn about all of them. We hope that the knowledge and
thinking processes that you have used in this course will serve you well in
your future education, and will help you attain success in whatever
endeavor you choose for your future work.
Reflexes
When the body reacts involuntarily to an internal or external stimulus, the
response is called a reflex, and the neurons that make up the simple circuit
are called a reflex arc. This is involuntary, spontaneous, and does not
involve processing of stimuli by higher centers (e.g. regions of the brain).
Reflexes can be spinal or cranial, depending on the nerves and central
components that are involved. For example heat and pain sensations from a
hot stove causing withdrawal of the arm through a connection in the spinal
cord that leads to contraction of the muscles in the arm, jerking the arm
away from the hot stove.
Other examples of reflexes include
¢ Withdrawal reflex, which occurs when you step on a painful
stimulus, like a tack or a sharp rock. The pain receptors (nociceptors)
that are activated by the painful stimulus activate the motor neurons
responsible for contraction of the leg muscles to remove your foot
from the pain.
¢ Stretch reflex, which helps to maintain muscles and an optimal length.
Receptors (called spindle receptors) within muscles are activated when
the muscle is stretched, causing direct contraction of the muscle.
¢ Corneal reflex, or eye-blink reflex. When the cornea is stimulated,
whether by touch or a bright light, blinking of the eyelids is initiated.
Obviously this is to keep the cornea safe from abrasion by dust or
flying insects, etc, and to protect the lens and retina from over-bright
light. There are more nerves per square inch in your cornea than in any
other part of your body!
The autonomic nervous system regulates organ systems through circuits
that resemble the reflexes of the somatic nervous system such as the knee
jerk reflex. The main difference between the somatic and autonomic
systems is in what target tissues are effectors. Somatic responses are solely
based on skeletal muscle contraction. The autonomic system, however,
targets cardiac and smooth muscle, as well as glandular tissue. Whereas the
basic circuit is a reflex arc, there are differences in the structure of those
reflexes for the somatic and autonomic systems.
Components of the Reflex Arc
There are typically three neurons in a reflex arc. These are a sensory
neuron, which responds to a sensory stimulus (touch, pain, muscle stretch,
etc.); an interneuron, which receives a signal if the sensory neuron is
stimulated sufficiently; and a motor neuron, which is stimulated by the
interneuron and then carries out the action required for the stimulus which
initiated the response. The sensory neurons can be oriented externally (i.e.,
to detect stimuli coming from outside the body), in internally, to detect
stimuli originating in the body. An example of the latter would be the
stretch receptors that tell your stomach to start contracting harder after a big
meal, or the pressure receptors (baroreceptors) in your carotid arteries
which detect blood pressure and tell your heart to beat faster or slower,
according to the pressure that they are sensing. Similarly, the interneurons
fall into two general categories. In long reflexes, the interneuron is in a
central nervous system (CNS) structure such as the brain or spinal cord. In
short reflexes, the interneuron is located in a peripheral ganglion, bypassing
the CNS, as shown in [link]. Finally, the motor neurons which generates the
response can also be classified into two general categories. One type of
motor neuron innervates a muscle, and stimulates contraction of that
muscle, and the subsequent rapid removal of your hand from a hot stove, or
a more rapid heartbeat, for example. The second class innervates a gland,
and causes secretion of hormones that mediate the appropriate response. An
example of the latter would be the nerves which cause the adrenal gland to
release adrenaline as part of the fight-or-flight response when you see a lion
or tiger or bear coming at you.
Short and Long Reflexes
Short and Long Reflexes
Long Reflex
Sensory receptor cell
—
Sensory cell synapses os =i
in spinal cord or brain SES
} Z,
Short Reflex
Sensory receptor cell
oF =-5- pe (« Sensation
Sensory cell synapses only
in peripheral ganglion
Sensory input can stimulate either a short or a long reflex.
A sensory neuron can project to the CNS or to an
autonomic ganglion. The short reflex involves the direct
stimulation of a postganglionic fiber by the sensory neuron,
whereas the long reflex involves integration in the spinal
cord or brain.
Homeostasis
As we come to the end of this module, it is appropriate to revisit the
concept of homeostasis as a unifying theme in biology. The reflexes
described above are just one example homeostatic mechanisms that allow
organisms to maintain the parameters of their internal environment about an
optimal setting. The organ systems described in this section also all have
many examples of homeostatic mechanisms that allow those organ systems
to maintain optimal levels of other parameters, such as oxygen levels in the
blood, or the pH of the contents of the duodenum. All of these organ
systems work together for the benefit, survival and reproduction of the
organism. The organ systems are highly interconnected as well. The
circulatory and respiratory systems must coordinate their functions, since
the function of one is to circulate the needed gases and waste products that
come in and go out via the other system. The osmoregulatory system also
has to work hand-in-hand with the circulatory and respiratory system to
maintain the content of the blood at optimal levels, the digestive system has
to provide the nutrients for all of these other organs to function, the nervous
and endocrine systems have to respond to a variety of external and internal
signals, etc. Finally, the organisms that compose populations and
communities and ecosystems also seem to interact with the abiotic
components (e.g. nutrients) of the ecosystem in a homeostatic fashion; for
example, the CO, needed by plants is emitted by other organisms, and the
level of atmospheric CO, has remained relatively constant over many
millenia.
But it is becoming ever more clear that the activities of one species on the
planet, Homo sapiens, is resetting the set points for these homeostatic
processes. As we currently burn about a million years worth of past net
primary productivity every year, we are seeing the atmospheric CO) levels
slowly rise, as you learned in an earlier module. The effects of changing the
amount of that globally important compound, over a short time span,
geologically speaking, are just starting to be realized. But it is clear that
there will be many ramifications, even if we don't yet understand all of
them. It is hoped that your newfound understanding of biological
interactions and homeostatic mechanisms will enable your generation to
devise appropriate strategies that will again demonstrate that the "sapiens"
part of our name is a good descriptor for our species. It will take both the
knowledge you have gained in this class, and the wisdom you will gain in
all your classes and experiences, to meet the challenges ahead.
Viruses
Introduction
"That's the salubrious thing about zoonotic diseases: they remind us, as
Saint Francis did, that we humans are inseparable from the natural world. In
fact, there is no "natural world", its a bad and artificial phrase. There is only
the world. Humankind is part of that world, as are the ebola viruses, as are
the influenzas and the HIVs, as are Marburg and Nipah and SARS, as are
chimpanzees and palm civets and Egyptian fruit bats, as is the next
murderous virus - the one we haven't yet discovered." David Quammen,
(a) The tobacco mosaic virus, seen by transmission
electron microscopy, was the first virus to be
discovered. (b) The leaves of an infected plant are
shown. (credit a: scale-bar data from Matt Russell;
credit b: modification of work by USDA, Department
of Plant Pathology Archive, North Carolina State
University)
No one knows exactly when viruses emerged or from where they came,
since viruses do not leave physical evidence in the form of fossils. Modern
viruses are thought to be a mosaic of bits and pieces of nucleic acids picked
up from various sources along their respective evolutionary paths. Viruses
are acellular, parasitic entities that are not classified within any of the three
domains because they are not exactly alive. But they do parasitize, evolve,
reproduce and co-evolve with other organisms; they inhabit a shadowy
world that may not be alive, but is very close to it. They have no plasma
membrane, internal organelles, or metabolic processes, and they do not
divide. Instead, they infect a host cell and use the host’s replication
processes to produce progeny virus particles. Viruses infect all forms of
organisms including bacteria, archaea, fungi, plants, and animals.
Viruses are diverse. They vary in their structure, their replication methods,
and in their target hosts or even host cells. They infect every type of
organism known, from Archaea to Bacteria to Eukaryotes, and are found in
every environment. They are also remarkably abundant; it is estimated that
each milliliter of sea water contains 10” viruses, both DNA and RNA
varieties. They are major players in the evolution of the life forms on this
planet; genes derived from viruses allowed mammals to develop a placenta,
for example.
How Viruses Replicate
Viruses were first discovered after the development of a porcelain filter,
called the Chamberland-Pasteur filter, which could remove all bacteria
visible under the microscope from any liquid sample. In 1886, Adolph
Meyer demonstrated that a disease of tobacco plants, tobacco mosaic
disease, could be transferred from a diseased plant to a healthy one through
liquid plant extracts. In 1892, Dmitri Ivanowski showed that this disease
could be transmitted in this way even after the Chamberland-Pasteur filter
had removed all viable bacteria from the extract. Still, it was many years
before it was proven that these “filterable” infectious agents were not
simply very small bacteria but were a new type of tiny, disease-causing
particle.
Virions, single virus particles, are very small, about 20—250 nanometers (1
nanometer = 1/1,000,000 mm); although the recent discovery of entities
called Pandoraviruses (approx 1 micrometer, or 1/1,000 mm in diameter)
has shaken that paradigm somewhat. Individual virus particles are the
infectious form of a virus outside the host cell. Unlike bacteria (which are
about 100 times larger), we cannot see most viruses with a light
microscope, with the exception of the Pandoraviruses and some large
virions of the poxvirus family ([link]).
Pollen
it f Flu virus
304 C60 Protein
Lipids
Atom
Plant cell
Relatives sizes on a logarithmic scale
0..nm inm 10 nm 100 nm ium 10 um 100 pm 1mm
Light microscope
Electron microscope
The size of a virus is very small relative to the size of
cells and organelles.
It was not until the development of the electron microscope in the 1940s
that scientists got their first good view of the structure of the tobacco
mosaic virus ({link]) and others. The surface structure of virions can be
observed by both scanning and transmission electron microscopy, whereas
the internal structures of the virus can only be observed in images from a
transmission electron microscope ((link]).
The ebola virus is shown here as visualized
through (a) a scanning electron micrograph and
(b) a transmission electron micrograph. (credit
a: modification of work by Cynthia Goldsmith,
CDC; credit b: modification of work by
Thomas W. Geisbert, Boston University
School of Medicine; scale-bar data from Matt
Russell)
The use of this technology has allowed for the discovery of many viruses of
all types of living organisms. They were initially grouped by shared
morphology, meaning their size, shape, and distinguishing structures. Later,
groups of viruses were classified by the type of nucleic acid they contained,
DNA or RNA, and whether their nucleic acid was single- or double-
stranded. More recently, molecular analysis of viral replication cycles has
further refined their classification. Currently virus classification begins at
the level of Order, and proceeds to species level taxonomy using this
scheme. The terms in parentheses are the taxon suffixes for that taxonomic
level.
Virus classification
e Order (-virales)
e Family (-viridae)
e Subfamily (-virinae)
e Genus (-virus)
e Species (usually XX XX (disease) virus, e.g., Tobacco Mosaic Virus)
A virion consists of a nucleic-acid core, an outer protein coating, and
sometimes an outer envelope made of protein and phospholipids derived
from the host cell. The most visible difference between members of viral
families is their morphology, which is quite diverse. An interesting feature
of viral complexity is that the complexity of the host does not correlate to
the complexity of the virion. Some of the most complex virion structures
are observed in bacteriophages, viruses that infect the simplest living
organisms, bacteria.
Viruses come in many shapes and sizes, but these are consistent and distinct
for each viral family ({link]). All virions have a nucleic-acid genome
covered by a protective layer of protein, called a capsid. The capsid is made
of protein subunits called capsomeres. Some viral capsids are simple
polyhedral “spheres,” whereas others are quite complex in structure. The
outer structure surrounding the capsid of some viruses is called the viral
envelope. All viruses use some sort of glycoprotein to attach to their host
cells at molecules on the cell called viral receptors. The virus exploits these
cell-surface molecules, which the cell uses for some other purpose, as a way
to recognize and infect specific cell types.
The T4 bacteriophage, which infects the E. coli bacterium, is among the
most complex virions known; T4 has a protein tail structure that the virus
uses to attach to the host cell and a head structure that houses its DNA.
Adenovirus, a nonenveloped animal virus that causes respiratory illnesses
in humans, uses protein spikes protruding from its capsomeres to attach to
the host cell. Nonenveloped viruses also include those that cause polio
(poliovirus), plantar warts (papillomavirus), and hepatitis A (hepatitis A
virus). Nonenveloped viruses tend to be more robust and more likely to
survive under harsh conditions, such as the gut.
Enveloped virions like HIV (human immunodeficiency virus), the causative
agent in AIDS (acquired immune deficiency syndrome), consist of nucleic
acid (RNA in the case of HIV) and capsid proteins surrounded by a
phospholipid bilayer envelope and its associated proteins ({link]). Chicken
pox, influenza, and mumps are examples of diseases caused by viruses with
envelopes. Because of the fragility of the envelope, nonenveloped viruses
are more resistant to changes in temperature, pH, and some disinfectants
than enveloped viruses.
Overall, the shape of the virion and the presence or absence of an envelope
tells us little about what diseases the viruses may cause or what species they
might infect, but is still a useful means to begin viral classification.
Bacteriophage T4
Adenovirus
Glycoproteins Capsomere
Tail fibers Reverse
transcriptase
Viruses can be complex in shape or
relatively simple. This figure shows
three relatively complex virions: the
bacteriophage T4, with its DNA-
containing head group and tail fibers
that attach to host cells; adenovirus,
which uses spikes from its capsid to
bind to the host cells; and HIV, which
uses glycoproteins embedded in its
envelope to do so. Notice that HIV
has proteins called matrix proteins,
internal to the envelope, which help
stabilize virion shape. HIV is a
retrovirus, which means it reverse
transcribes its RNA genome into
DNA, which is then spliced into the
host’s DNA. (credit “bacteriophage,
adenovirus”: modification of work by
NCBI, NIH; credit “HIV retrovirus”:
modification of work by NIAID, NIH)
Unlike all living organisms that use DNA as their genetic material, viruses
may use either DNA or RNA as theirs. The virus core contains the genome
or total genetic content of the virus. Viral genomes tend to be small
compared to bacteria or eukaryotes, containing only those genes that code
for proteins the virus cannot get from the host cell. This genetic material
may be single-stranded or double-stranded. It may also be linear or circular.
While most viruses contain a single segment of nucleic acid, others have
genomes that consist of several segments. All of these features are used to
help classify viruses into orders, families, etc.
DNA viruses have a DNA core. The viral DNA directs the host cell’s
replication proteins to synthesize new copies of the viral genome and to
transcribe and translate that genome into viral proteins. DNA viruses cause
human diseases such as chickenpox, hepatitis B, and some venereal
diseases like herpes and genital warts.
RNA viruses contain only RNA in their cores. To replicate their genomes in
the host cell, the genomes of RNA viruses encode enzymes not found in
host cells. RNA polymerase enzymes are not as stable as DNA polymerases
and often make mistakes during transcription. For this reason, mutations,
changes in the nucleotide sequence, in RNA viruses occur more frequently
than in DNA viruses. This leads to more rapid evolution and change in
RNA viruses. For example, the fact that influenza is an RNA virus is one
reason a new flu vaccine is needed every year; rapid evolution results in
new flu strains being produced constantly in various parts of the world.
Human diseases caused by RNA viruses include hepatitis, measles, HIV,
common cold virus, Ebola and rabies.
Steps of Virus Infections
Viruses are specialized parasites, usually only infecting one type of cell or
one type of organism. A virus must “take over” a cell to replicate. The viral
replication cycle can produce dramatic biochemical and structural changes
in the host cell, which may cause cell damage. These changes, called
cytopathic effects, can change cell functions or even destroy the cell. Some
infected cells, such as those infected by the common cold virus (rhinovirus),
die through lysis (bursting) or apoptosis (programmed cell death or “cell
suicide”), releasing all the progeny virions at once. The symptoms of these
viral diseases result from the immune response to the virus, which attempts
to control and eliminate the virus from the body, and from cell damage
caused by the virus. Many animal viruses, such as HIV (human
immunodeficiency virus), leave the infected cells of the immune system by
a process known as budding, where virions leave the cell individually.
During the budding process, the cell does not undergo lysis and is not
immediately killed. However, the damage to the cells that HIV infects may
make it impossible for the cells to function as mediators of immunity, even
though the cells remain alive for a period of time. Most productive viral
infections follow similar steps in the ,virus replication cycle : attachment,
penetration, uncoating, replication, assembly, and release.
A virus attaches to a specific receptor site on the host-plasma membrane
through attachment proteins in the capsid or proteins embedded in its
envelope. The attachment is specific, and typically a virus will only attach
to cells of one or a few species and only certain cell types within those
species with the appropriate receptors.
The nucleic acid of bacteriophages is injected directly into the host cell,
leaving the capsid outside the cell. Plant and animal viruses can enter their
cells through endocytosis, in which the plasma membrane surrounds and
engulfs the entire virus. Some enveloped viruses enter the cell when the
viral envelope fuses directly with the plasma membrane. Once inside the
cell, the viral capsid is degraded and the viral nucleic acid is released,
which then becomes available for replication and transcription. Obviously,
the naked DNA of a bacteriophage is already available for transcription and
replication immediately after being injected into the bacterial cell.
The replication mechanism depends on the viral genome (DNA or RNA).
DNA viruses usually use host cell proteins and enzymes to make additional
DNA that is then used to copy the genome or be transcribed to messenger
RNA (mRNA). The mRNA is then used in protein synthesis. RNA viruses,
such as the influenza virus, usually use the RNA as a template for synthesis
of viral genomic RNA and mRNA. The viral mRNA is translated into viral
enzymes and capsid proteins to assemble new virions ((link]).
The last stage of viral replication is the release of the new virions into the
host organism, where they are able to infect adjacent cells and repeat the
replication cycle. Some viruses are released when the host cell dies and
other viruses can leave infected cells by budding through the membrane
without directly killing the cell.
Influenza virus
Nucleus
Receptor
Epithelial cell ty
The cell
engulfs
: the virus by
@ Influenza virus becomes endocytosis.
attached to a target
epithelial cell.
® New viral particles are made and Viral MRNA is used to @ Viral contents are released.
released into the extracellular fluid. make viral proteins. Viral RNA enters the nucleus
The cell, which is not killed in the where it is replicated by the
process, continues to make new virus. viral RNA polymerase.
In influenza virus infection, glycoproteins attach to
a host epithelial cell. As a result, the virus is
engulfed. RNA and proteins are made and
assembled into new virions.
Lytic and Lysogenic Pathways
Cell death may be immediate or delayed after attachment and penetration
by the virus. For example, bacteriophages, viruses that infect bacteria, may
or may not kill their host immediately. There are two viral replication
strategies; when the virus kills the host cell it is called the lytic cycle, and
when the virus does not kill the host but replicates when the host replicates
it is called the lysogenic cycle ((link)).
Lytic Attach to host Lysogenic
& inject DNA
When triggered,
the virus
becomes active
Host cell and
viral DNA
replicate and
divide
Host cell lyses and
viruses are released
New viral components Viral DNA integrates
constructed into host
chromosomes
The two viral reproductive strategies, the lytic cycle and
the lysogenic cycle
Lytic cycle
The lytic cycle causes death of the host cell and the term refers to the last
stage of the infection when the cell lyses (breaks open) and releases new
virions that were produced within the cell. These new virions can infect
healthy cells and the cycle is repeated ({link]).
So why haven't all the bacteria in the world been destroy by
bacteriophages? The answer is natural selection of defense mechanisms by
bacteria. Mutations of bacterial surface proteins that are not recognized by a
particular phage allow the bacteria to survive by preventing attachment.
Without going into detail, bacteria have internal defenses that allow them to
cut up viral DNA before it can infect the cell. Then one might ask, why
hasn't all the bacteriophages in the world gone extinct by not being able to
reproduce. Once again, the answer is natural selection. Viruses mutate to
bypass the defense mechanisms of the bacteria. This illustrates that the
parasite-host relationship is in a constant evolutionary duel.Similar co-
evolutionary strategies characterize the interactions of viruses and animals,
or viruses and plants.
Lysogenic cycle
There is another reason why bacteria are not extinct because of
bacteriophages. Many bacteriophages do not kill their host but coexist
within their host, and when this occurs it is called the lysogenic cycle. After
penetration, the viral DNA or RNA can either be incorporated into the host
DNA, or the viral genome can be a self-replicating entity. Once this occurs,
the viral genome is replicated along with the host cell's DNA, but the virus
does not destroy the cell as it does in the lytic cycle ({link]). However, at
some point the viral genes are turned on and can trigger the virus to enter
the lytic cycle and kill the host cell ({link]). Cell starvation or cell damage
(e.g. from radiation) may trigger a lysogenic infection to turn into a lytic
infection thereby killing the host cell. The next generation of viruses,
depending on the host cell condition, can use either of the viral replication
Strategies, lysogenic or lytic, on the next host.
Viruses and Disease
Viruses cause a variety of diseases in animals, including humans, ranging
from the common cold to potentially fatal illnesses like meningitis ([link]).
These diseases can be treated by antiviral drugs or by vaccines, but some
viruses, such as HIV, are capable of avoiding the immune response and
mutating so as to become resistant to antiviral drugs.
Overview of Viral Infections
Encephalitis/
meningitis
- JC virus
Common cold
- Rhinoviruses
- Measles - Parainfluenza virus
- LCM virus - Respiratory syncytial
- Arbovirus virus
- Rabies
Gingivostomatitis
- Herpes simplex type 1
Pharyngitis
- Adenovirus
- Epstein-Barr virus
- Cytomegalovirus
Cardiovascular
- Coxsackie B virus
Hepatitis
- Hepatitis virus
types A, B, C, D, andE
Skin infections
- Varicella-zoster virus
- Human herpesvirus 6
- Smallpox
- Molluscum contagiosum
- Human papillomavirus
- Parvovirus B19
- Rubella - Herpes simplex type 2
- Measles - Human papillomavirus
- Coxsackie A virus - HIV
Sexually transmitted
diseases
Eye infections
- Herpes simplex virus
- Adenovirus
- Cytomegalovirus
Parotitis -;Pneumonia
- Influenza virus
types A and B
- Parainfluenza
virus
- Respiratory
syncytial virus
- Adenovirus
- SARS coronavirus
Myelitis
- Poliovirus
- HTLV-I
Gastroenteritis
- Adenovirus
- Rotavirus
- Norovirus
- Astrovirus
- Coronavirus
Pancreatitis
- Coxsackie B virus
Viruses are the cause of dozens of ailments
in humans, ranging from mild illnesses to
serious diseases. (credit: modification of
work by Mikael Haggstr6m)
Innate Immunity
Introduction
"The organism possesses certain contrivances by means of which the
immunity reaction, so easily produced by all kinds of cells, is prevented
from acting against the organism's own elements and so giving rise to
autotoxins... These contrivances are naturally of the highest importance for
the existence of the individual." Paul Ehrlich, German immunologist and
pharmacologist, "On Hemolysins", 1901
Although other organisms have immune responses of various types, the
vertebrate immune system is the most sophisticated. The vertebrate immune
system is a complex multilayered system for defending against external and
internal threats to the integrity of the body. The system can be divided into
two types of defense systems: the innate immune system, which is
nonspecific toward a particular kind of pathogen, and the adaptive immune
system, which is specific ((link]). Innate immunity relies on physical and
chemical barriers that work on all pathogens, sometimes called the first line
of defense. The second line of defense of the innate system includes
chemical signals that produce inflammation and fever responses as well as
mobilizing protective cells and other chemical defenses. The adaptive
immune system mounts a highly specific response to substances and
organisms that do not belong in the body. The adaptive system takes longer
to respond and has a memory system that allows it to respond with greater
intensity should the body re-encounter a pathogen, even years later. That
memory is the basis for the long-term effectiveness of many vaccines.
Vertebrate Immunity
Innate Immune System Adaptive Immune System
Physical Barriers Internal Defenses
+ Skin, hair, cilia + Inflammatory response + Antibodies and the humoral immune response
* Mucus membranes * Complement proteins * Cell-mediated immune response
* Mucus and chemical secretions * Phagocytic cells * Memory response
* Digestive enzymes in mouth « Natural killer (NK) cells
* Stomach acid
There are two main parts to the vertebrate immune system. The
innate immune system, which is made up of physical barriers
and internal defenses, responds to all pathogens. The adaptive
immune system is highly specific.
External and Chemical Barriers
The body has significant physical barriers to potential pathogens. The skin
contains the protein keratin, which resists physical entry into cells. Other
body surfaces, particularly those associated with body openings, are
protected by the mucous membranes. The sticky mucus provides a physical
trap for pathogens, preventing their movement deeper into the body. Some
openings of the body, such as the nose and ears, are protected by hairs that
catch pathogens, and the mucous membranes of the upper respiratory tract
have cilia that constantly sweep pathogens trapped in the mucus coat up to
the mouth. The skin and mucous membranes also create a chemical
environment that is hostile to many microorganisms. The surface of the skin
is acidic, which prevents bacterial growth. Saliva, mucus, and the tears of
the eye contain an enzyme that breaks down bacterial cell walls. The
stomach secretions create a highly acidic environment, which kills many
pathogens entering the digestive system.
Finally, the surface of the body and the lower digestive system have a
community of commensal microorganisms such as bacteria, archaea, and
fungi (the microbiome) that coexist without harming the body. There is
evidence that these organisms are highly beneficial to their host, combating
disease-causing organisms and outcompeting them for nutritional resources
provided by the host body. Despite these defenses, pathogens may enter the
body through skin abrasions or punctures, or by collecting on mucosal
surfaces in large numbers that overcome the protections of mucus or cilia.
Internal Defenses
If pathogens defeat these defenses and enter the body, the innate immune
system responds with a variety of internal defenses. These include the
inflammatory response, phagocytosis, natural killer cells, and the
complement system. White blood cells in the blood and lymph recognize
pathogens as foreign to the body. A white blood cell is larger than a red
blood cell, is nucleated, and is typically able to move using amoeboid
locomotion. Because they can move on their own, white blood cells can
leave the blood to go to infected tissues. For example, a monocyte is a type
of white blood cell that circulates in the blood and lymph and develops into
a macrophage after it moves into infected tissue. A macrophage is a large
phagocytic cell that engulfs and devours foreign particles and pathogens.
Once a pathogen is recognized as foreign and devoured by a macrophage,
chemicals called cytokines are released. A cytokine is a chemical
messenger that regulates cell differentiation (form and function),
proliferation (production), and gene expression to produce a variety of
immune responses. Approximately 40 types of cytokines exist in humans.
In addition to being released from white blood cells after pathogen
recognition, cytokines are also released by the infected cells and bind to
nearby uninfected cells, inducing those cells to release cytokines. This
positive feedback loop results in a burst of cytokine production.
One class of early-acting cytokines is the interferons, which are released by
infected cells as a warning to nearby uninfected cells. An interferon is a
small protein that signals a viral infection to other cells. The interferons
stimulate uninfected cells to produce compounds that interfere with viral
replication. Interferons also activate macrophages and other cells.
The Inflammatory Response and Phagocytosis
The first cytokines to be produced encourage inflammation, a localized
redness, swelling, heat, and pain. Inflammation is a response to physical
trauma, such as a cut or a blow, chemical irritation, and infection by
pathogens (viruses, bacteria, or fungi). The chemical signals that trigger an
inflammatory response enter the extracellular fluid and cause capillaries to
dilate (expand) and capillary walls to become more permeable, or leaky.
The serum and other compounds leaking from capillaries cause swelling of
the area, which in turn causes pain. Various kinds of white blood cells are
attracted by the cytokines released at the area of inflammation. The types of
white blood cells that arrive at an inflamed site depend on the nature of the
injury or infecting pathogen. For example, a neutrophil is an early arriving
white blood cell that engulfs and digests pathogens. Neutrophils are the
most abundant white blood cells of the immune system ((Link]).
Macrophages follow neutrophils and take over the phagocytosis function
and are involved in cleaning up cell debris and pathogens.
White blood cells
(leukocytes) release
chemicals to stimulate
the inflammatory
response following a
cut in the skin.
Cytokines also send feedback to cells of the nervous system to bring about
the overall symptoms of feeling sick, which include lethargy, muscle pain,
and nausea. Cytokines can thus increase the core body temperature, causing
a fever. The elevated temperatures of a fever inhibit the growth of
pathogens and speed up cellular repair processes. For these reasons,
suppression of fevers should be limited to those that are dangerously high.
Natural Killer Cells
A lymphocyte is a white blood cell that contains a large nucleus ((link]).
Most lymphocytes are associated with the adaptive immune response, but a
class of lymphocytes known as natural killer cells are part of the innate
immune system. Unlike other white blood cells that attack invading bacteria
or fungi, natural killer (NK) cell is a lymphocyte. Natural killer cells kill
body cells that are infected with viruses (or cancerous cells). NK cells
identify intracellular infections, especially from viruses, and attack the
infected cells, destroying them so that they cannot release more viruses.
eo
5 yum
i,
Lymphocytes, such
as NK cells, are
characterized by
their large nuclei
that actively absorb
Wright stain and
therefore appear
dark colored under
a microscope.
(credit: scale-bar
data from Matt
Russell)
Mast cell Natural killer cell Monocyte Macrophage Neutrophil
Cells involved in the innate immune response include mast
cells, natural killer cells, and white blood cells, such as
monocytes, macrophages and neutrophils.
Complement
An array of approximately 20 types of proteins, called a complement
system, is also activated by infection or the activity of the cells of the
adaptive immune system and functions to destroy extracellular pathogens.
Liver cells and macrophages synthesize inactive forms of complement
proteins continuously; these proteins are abundant in the blood serum and
are capable of responding immediately to infecting microorganisms. The
complement system is so named because it is complementary to the innate
and adaptive immune system. Complement proteins bind to the surfaces of
microorganisms and are particularly attracted to pathogens that are already
tagged by the adaptive immune system. This “tagging” involves the
attachment of specific proteins called antibodies (discussed in detail later)
to the pathogen. When they attach, the antibodies change shape providing a
binding site for one of the complement proteins. After the first few
complement proteins bind, a cascade of binding in a specific sequence of
proteins follows in which the pathogen rapidly becomes coated in
complement proteins.
Complement proteins perform several functions, one of which is to serve as
a marker to indicate the presence of a pathogen to phagocytic cells and
enhance engulfment. Certain complement proteins can combine to open
pores in microbial plasma membranes, causing ion leakage and lysis of the
microbial cells.
Adaptive Immunity
Introduction
"An immune system of enormous complexity is present in all vertebrate
animals. When we place a population of lymphocytes from such an animal
in appropriate tissue culture fluid, and when we add an antigen, the
lymphocytes will produce specific antibody molecules, in the absense of
any nerve cells. I find it astonishing that the immune system embodies a
degree of complexity which suggests some more or less superficial though
striking analogies with human language, and that this cognitive system has
evolved and functions without assistance of the brain." Niels K. Jerne,
Danish immunologist, "The Generative Grammar of the Immune System",
Nobel Lecture, 1984
The adaptive, or acquired, immune response takes days or even weeks to
become established—much longer than the innate response; however,
adaptive immunity is more specific to an invading pathogen. Adaptive
immunity is an immunity that occurs after exposure to an antigen either
from a pathogen or a vaccination. An antigen is a molecule that stimulates
a response in the immune system. This part of the immune system is
activated when the innate immune response is insufficient to control an
infection. In fact, without information from the innate immune system, the
adaptive response could not be mobilized. There are two types of adaptive
responses: the cell-mediated immune response, which is controlled by
activated T cells, and the humoral immune response, which is controlled
by activated B cells and antibodies. Activated T and B cells, which
specifically bind to molecules from the invading pathogen, attack the
pathogen specifically. These cells can kill pathogens directly, or they can
secrete antibodies that enhance the phagocytosis of pathogens and disrupt
the infection. Adaptive immunity also involves a memory to give the host
long-term protection from reinfection with the same type of pathogen; on
reexposure, this host memory will facilitate a rapid and powerful response.
B and T Cells
Lymphocytes, which are white blood cells, are formed with other blood
cells in the red bone marrow. The two types of lymphocytes of the adaptive
immune response are B and T cells ({link]). Whether an immature
lymphocyte becomes a B cell or T cell depends on where in the body it
matures. The B cells remain in the bone marrow to mature (hence the name
“B” for “bone marrow”), while T cells migrate to the thymus, where they
mature (hence the name “T” for “thymus”).
Maturation of a B or T cell involves becoming immunocompetent, meaning
that it can recognize, by binding, a specific molecule or antigen (discussed
below). During the maturation process, B and T cells that bind too strongly
to the body’s own cells are eliminated in order to minimize an immune
response against the body’s own tissues. Those cells that react weakly or
not at all to the body’s own cells, but have highly specific receptors on their
cell surfaces that allow them to recognize a foreign molecule, or antigen,
remain. This process occurs during fetal development and continues
throughout life. The specificity of this receptor is determined by the
genetics of the individual and is present before a foreign molecule is
introduced to the body or encountered. Thus, it is genetics and not
experience that initially provides a vast array of cells, each capable of
binding to a different specific foreign molecule. Once they are
immunocompetent, the T and B cells will migrate to the spleen and lymph
nodes where they will remain until they are called on during an infection. B
cells are involved in the humoral immune response, which targets
pathogens found in blood and lymph, and T cells are involved in the cell-
mediated immune response, which targets infected body cells.
This scanning electron
micrograph shows a T
lymphocyte. T and B
cells are indistinguishable
by light microscopy but
can be differentiated
experimentally by
probing their surface
receptors. (credit:
modification of work by
NCI; scale-bar data from
Matt Russell)
Humoral Immune Response
As mentioned, an antigen is a molecule that stimulates a response in the
immune system. B cells participate in a chemical response to new antigens
by producing specific antibodies that circulate throughout the body and
bind with the antigen whenever it is encountered. This is known as the
humoral immune response, because the active molecule is secreted into
the body fluids, or "humours". As discussed, during maturation of B cells, a
set of highly specific B cells are produced that have many antigen receptor
molecules in their membrane ((link]).
Antigens
Antigen
y Antigen-binding site
B cell receptors are
embedded in the
membranes of B
cells and bind a
variety of antigens
through their
variable regions.
Each B cell has only one kind of antigen receptor, which makes every B cell
different. Once the B cells mature in the bone marrow, they migrate to
lymph nodes or other lymphatic organs. When a B cell encounters the
antigen that binds to its receptor, the antigen molecule is brought into the
cell by endocytosis. It is digested in the lysosomes, and fragments of the
foreign molecule are then displayed on the surface of the B cell. These
displayed molecules can activate other cells as part of the immune response.
When this process is complete, the B cell is sensitized. In most cases, the
sensitized B cell must then encounter a specific kind of T cell, called a
helper T cell, before it is activated. The helper T cell must already have
been activated through an encounter with the antigen (discussed below).
The helper T cell binds to the displayed antigen fragments on the B cell,
and is activated to release cytokines that induce the B cell to divide rapidly.
This generates thousands of identical (clonal) B cells. These daughter cells
have two possible fates: they can become either plasma cells or memory B
cells. The plasma cells produce and secrete large quantities of antibody
molecules, up to 100 million molecules per hour, . An antibody, also
known as an immunoglobulin (Ig), is a protein that is produced by plasma
cells after stimulation by an antigen. Antibodies are the agents of humoral
immunity. Antibodies occur in the blood, in gastric and mucus secretions,
and in breast milk. Antibodies in these bodily fluids can bind pathogens and
mark them for destruction by phagocytes before they can infect cells. The
memory B cells become quiescent, and only become reactivated after
another later encounter with the antigen. This can be caused by a reinfection
by the same bacteria or virus, and activation of the memory cells again
results in a new population of antibody-producing plasma cells to fight the
re-infection.
These antibodies circulate in the blood stream and lymphatic system and
bind with the antigen whenever it is encountered. The binding can fight
infection in several ways. Antibodies can bind to viruses or bacteria and
interfere with the chemical interactions required for them to infect or bind
to other cells. The antibodies may create bridges between different particles
containing antigenic sites clumping them all together and preventing their
proper functioning. The antigen-antibody complex stimulates the
complement system described previously, destroying the cell bearing the
antigen. Phagocytic cells, such as those already described, are attracted by
the antigen-antibody complexes, and phagocytosis is enhanced when the
complexes are present. Finally, antibodies stimulate inflammation, and their
presence in mucus and on the skin prevents pathogen attack.
Antibodies coat extracellular pathogens and neutralize them by blocking
key sites on the pathogen that enhance their infectivity (such as receptors
that “dock” pathogens on host cells) ({link]). Antibody neutralization can
prevent pathogens from entering and infecting host cells. The neutralized
antibody-coated pathogens can then be filtered by the spleen and destroyed.
Antibodies also mark pathogens for destruction by phagocytic cells, such as
macrophages or neutrophils, in a process called opsonization. In a process
called complement fixation, some antibodies provide a place for
complement proteins to bind. The combination of antibodies and
complement promotes rapid clearing of pathogens.
The production of antibodies by plasma cells in response to an antigen is
called active immunity and describes the host’s active immune response to
an infection or to a vaccination. There is also a passive immune response
where antibodies come from an outside source, instead of the individual’s
own plasma cells, and are introduced into the host. For example, antibodies
circulating in a pregnant woman’s body move across the placenta into the
developing fetus. The child benefits from the presence of these antibodies
for up to several months after birth. In addition, a passive immune response
is possible by injecting antibodies into an individual in the form of an
antivenom to a snake-bite toxin or antibodies in blood serum to help fight a
hepatitis infection. This gives immediate protection since the body does not
need the time required to mount its own response.
(a) Neutralization Antibodies prevent a virus or toxic protein
from binding their target.
Antibody
Virus
Diptheria toxin
(b) Opsonization A pathogen tagged by antibodies is consumed
by a macrophage or neutrophil.
Macrophage
Pathogen
(c) Complement activation Antibodies attached to the surface
of a pathogen cell activate the complement system.
Pores formed
by complement
Antibodies may inhibit infection
by (a) preventing the antigen
from binding its target, (b)
tagging a pathogen for
destruction by macrophages or
neutrophils, or (c) activating the
complement cascade.
Cell-Mediated Immunity
Unlike B cells, T lymphocytes are unable to recognize pathogens without
assistance. Instead, dendritic cells and macrophages first engulf and digest
pathogens into hundreds or thousands of antigens. Then, an antigen-
presenting cell (APC) detects, engulfs, and informs the adaptive immune
response about an infection. When a pathogen is detected, these APCs will
engulf and break it down through phagocytosis. Antigen fragments will
then be transported to the surface of the APC, where they will serve as an
indicator to other immune cells. A dendritic cell is an immune cell that
mops up antigenic materials in its surroundings and presents them on its
surface. Dendritic cells are located in the skin, the linings of the nose, lungs,
stomach, and intestines. These positions are ideal locations to encounter
invading pathogens. Once they are activated by pathogens and mature to
become APCs they migrate to the spleen or a lymph node. Macrophages
also function as APCs. In all cases the foreign antigen is digested inside the
cell, and fragments of the antigen are then displayed on the surface of the
APC.
(4) Abacterium
engulfed by a
macrophage is
encased ina
vacuole. (2) Lysosomes fuse
with the vacuole
and digest the
Antigen bacterium.
Macrophage
(3) Antigens from digested
bacterium are presented with
MHC II on the cell surface.
An antigen-presenting cell
(APC), such as a macrophage,
engulfs a foreign antigen,
partially digests it in a lysosome,
and then displays it at the cell
surface. Lymphocytes of the
adaptive immune response must
interact with these displayed
fragments, bound to a specific
protein on the APC cell surface,
in order to mature into
functional immune cells.
T cells have many functions. Some respond to APCs of the innate immune
system and indirectly induce immune responses by releasing cytokines.
Others stimulate B cells to start the humoral response as described
previously. Another type of T cell detects APC signals and directly kills the
infected cells, while some are involved in suppressing inappropriate
immune reactions to harmless or “self” antigens.
There are two main types of T cells: helper T lymphocytes (T}) and the
cytotoxic T lymphocytes (Tc). The Ty lymphocytes function indirectly to
tell other immune cells about potential pathogens. Ty lymphocytes
recognize specific antigens presented by the MHC class II complexes of
APCs. There are two populations of Ty cells: Ty1 and Ty2. Ty1 cells
secrete cytokines to enhance the activities of macrophages and other T
cells. Ty2 cells stimulate naive B cells to secrete antibodies. Whether a Ty1
or a T}y2 immune response develops depends on the specific types of
cytokines secreted by cells of the innate immune system, which in turn
depends on the nature of the invading pathogen.
Cytotoxic T cells (T-) are the key component of the cell-mediated part of
the adaptive immune system and attack and destroy infected cells. Tc cells
are particularly important in protecting against viral infections; this is
because viruses replicate within cells where they are shielded from
extracellular contact with circulating antibodies. Once activated, the Tc
creates a large clone of cells with one specific set of cell-surface receptors,
as in the case with proliferation of activated B cells. As with B cells, the
clone includes active T¢ cells and inactive memory T¢ cells. The resulting
active Tc cells then identify infected host cells. Because of the time
required to generate a population of clonal T and B cells, there is a delay in
the adaptive immune response compared to the innate immune response.
Tc cells attempt to identify and destroy infected cells before the pathogen
can replicate and escape, thereby halting the progression of intracellular
infections. Tc cells also support NK lymphocytes to destroy early cancers.
Cytokines secreted by the Ty1 response that stimulates macrophages also
stimulate Tc cells and enhance their ability to identify and destroy infected
cells and tumors. A summary of how the humoral and cell-mediated
immune responses are activated appears in [link].
B plasma cells and T¢ cells are collectively called effector cells because
they are involved in “effecting” (bringing about) the immune response of
killing pathogens and infected host cells.
Bacterium
Antigen
Macrophage
Antigens from digested
bacterium are presented with
MHC II on the cell surface. In response to cytokines,
the T cell clones itself.
Activated
Humoral
helper T cell
immune
response
2 om, cell clones itself
Cell-mediated
immune
response
co Cytokines
Bee T cell becomes
Cytokines activate cytotoxic.
B cells and T cells
A helper T cell becomes activated by binding to an antigen
presented by an APC via the MHCII receptor, causing it to
release cytokines. Depending on the cytokines released, this
activates either the humoral or the cell-mediated immune
response.
Immunological Memory
The adaptive immune system has a memory component that allows for a
rapid and large response upon reinvasion of the same pathogen. During the
adaptive immune response to a pathogen that has not been encountered
before, known as the primary immune response, plasma cells secreting
antibodies and differentiated T cells increase, then plateau over time. As B
and T cells mature into effector cells, a subset of the naive populations
differentiates into B and T memory cells with the same antigen specificities
({link]). A memory cell is an antigen-specific B or T lymphocyte that does
not differentiate into an effector cell during the primary immune response,
but that can immediately become an effector cell on reexposure to the same
pathogen. As the infection is cleared and pathogenic stimuli subside, the
effectors are no longer needed and they undergo apoptosis. In contrast, the
memory cells persist in the circulation.
ee B cell receptor
Antigen on
bacterium
B cell
@
Memory B cells Plasma cells
After initially binding an antigen to
the B cell receptor, a B cell
internalizes the antigen and
presents it on MHC class IT. A
helper T cell recognizes the MHC
class IT- antigen complex and
activates the B cell. As a result,
memory B cells and plasma cells
are made.
If the pathogen is never encountered again during the individual’s lifetime,
B and T memory cells will circulate for a few years or even several decades
and will gradually die off, having never functioned as effector cells.
However, if the host is re-exposed to the same pathogen type, circulating
memory cells will immediately differentiate into plasma cells and T¢ cells
without input from APCs or Ty cells. This is known as the secondary
immune response. One reason why the adaptive immune response is
delayed is because it takes time for naive B and T cells with the appropriate
antigen specificities to be identified, activated, and proliferate. On
reinfection, this step is skipped, and the result is a more rapid production of
immune defenses. Memory B cells that differentiate into plasma cells
produce antibody at a level that is tens to hundreds-fold greater than during
the primary response ({link]). This rapid and dramatic antibody response
may stop the infection before it can even become established, and the
individual may not realize they had been exposed.
Antibody concentration ——»
Primary immune Secondary immune
response response
Time ——>
In the primary response to
infection, antibodies are
secreted first from plasma
cells. Upon re-exposure to
the same pathogen, memory
cells differentiate into
antibody-secreting plasma
cells that output a greater
amount of antibody for a
longer period of time.
Vaccination is based on the knowledge that exposure to noninfectious
antigens, derived from known pathogens, generates a mild primary immune
response. The immune response to vaccination may not be perceived by the
host as illness but still confers immune memory. When exposed to the
corresponding pathogen to which an individual was vaccinated, the reaction
is similar to a secondary exposure. Because each reinfection generates more
memory cells and increased resistance to the pathogen, some vaccine
courses involve one or more booster vaccinations to mimic repeat
exposures.
The Lymphatic System
Lymph is the watery fluid that bathes tissues and organs and contains
protective white blood cells but does not contain erythrocytes. Lymph
moves about the body through the lymphatic system, which is made up of
vessels, lymph ducts, lymph glands, and organs, such as tonsils, adenoids,
thymus, and spleen.
Although the immune system is characterized by circulating cells
throughout the body, the regulation, maturation, and intercommunication of
immune factors occur at specific sites. The blood circulates immune cells,
proteins, and other factors through the body. Approximately 0.1 percent of
all cells in the blood are leukocytes, which include monocytes (the
precursor of macrophages) and lymphocytes. Most cells in the blood are red
blood cells. Cells of the immune system can travel between the distinct
lymphatic and blood circulatory systems, which are separated by interstitial
space, by a process called extravasation (passing through to surrounding
tissue).
Recall that cells of the immune system originate from stem cells in the bone
marrow. B cell maturation occurs in the bone marrow, whereas progenitor
cells migrate from the bone marrow and develop and mature into naive T
cells in the organ called the thymus.
On maturation, T and B lymphocytes circulate to various destinations.
Lymph nodes scattered throughout the body house large populations of T
and B cells, dendritic cells, and macrophages ([link]). Lymph gathers
antigens as it drains from tissues. These antigens then are filtered through
lymph nodes before the lymph is returned to circulation. APCs in the lymph
nodes capture and process antigens and inform nearby lymphocytes about
potential pathogens.
Afferent lymphatic
vessel
Lymph
Efferent lymphatic
vessel
(b)
(a) Lymphatic vessels carry a clear fluid called
lymph throughout the body. The liquid passes
through (b) lymph nodes that filter the lymph
that enters the node through afferent vessels
and leaves through efferent vessels; lymph
nodes are filled with lymphocytes that purge
infecting cells. (credit a: modification of work
by NIH; credit b: modification of work by NCI,
NIH)
The spleen houses B and T cells, macrophages, dendritic cells, and NK cells
({link]). The spleen is the site where APCs that have trapped foreign
particles in the blood can communicate with lymphocytes. Antibodies are
synthesized and secreted by activated plasma cells in the spleen, and the
spleen filters foreign substances and antibody-complexed pathogens from
the blood. Functionally, the spleen is to the blood as lymph nodes are to the
lymph.
The spleen functions to
immunologically filter the
blood and allow for
communication between cells
corresponding to the innate
and adaptive immune
responses. (credit:
modification of work by NCI,
NIH)
Besides its close ties to and functions with the immune system, the
lymphatic system also serves a couple of other important functions. First,
the vessels of lymphatic system help absorb excess lymph from body
tissues and returns that lymph to the circulatory system via the lymphatic
ducts. This helps the body maintain fluid balance. The second function
deals with the absorption of lipids during digestion. The lymph vessels
located around the small intestine absorb the lacteals from the lumen of the
intestine and transport the lacteals to the circulatory system via the
lymphatic ducts. In this case the lymphatic system acts as a shuttle for
digested fats from the digestive system to the circulatory system.
Immune Tolerance
The immune system has to be regulated to prevent wasteful, unnecessary
responses to harmless substances, and more importantly, so that it does not
attack “self.” The acquired ability to prevent an unnecessary or harmful
immune response to a detected foreign substance known not to cause
disease, or self-antigens, is described as immune tolerance. The primary
mechanism for developing immune tolerance to self-antigens occurs during
the selection for weakly self-binding cells during T and B lymphocyte
maturation. There are populations of T cells that suppress the immune
response to self-antigens and that suppress the immune response after the
infection has cleared to minimize host cell damage induced by
inflammation and cell lysis. Immune tolerance is especially well developed
in the mucosa of the upper digestive system because of the tremendous
number of foreign substances (such as food proteins) that APCs of the oral
cavity, pharynx, and gastrointestinal mucosa encounter. Immune tolerance
is brought about by specialized APCs in the liver, lymph nodes, small
intestine, and lung that present harmless antigens to a diverse population of
regulatory T (Tyeg) cells, specialized lymphocytes that suppress local
inflammation and inhibit the secretion of stimulatory immune factors. The
combined result of Tyeg cells is to prevent immunologic activation and
inflammation in undesired tissue compartments and to allow the immune
system to focus on pathogens instead.
Urinary System
Introduction
" What is man, when you come to think upon him, but a minutely set,
ingenious machine for turning, with infinite artfulness, the red wine of
Shiraz into urine?" Baroness Karen Blixen, in The Dreamers, 1943
Osmoregulation and Osmotic Balance
Osmosis is the diffusion of water across a membrane in response to osmotic
pressure caused by differences in the solute molecules on either side of the
membrane. Osmoregulation is the active homeostatic process of the water
content of an organism, involving movement of solutes across membranes
so that water moves in response to the ion concentration . It might be
beneficial to review osmosis here - [link]. Osmo regulation involves control
of the water and solute content of all the fluids in the animal body. There
are three general fluid pools in the typical animal: the blood plasma, the
cytosol within cells, and the interstitial fluid (the fluid that exists in the
spaces between cells and tissues of the body). See [link] for a review of
how solute concentrations affect the movement of water across plasma
membranes.
Hypertonic Isotonic Hypotonic
HO
—e
Cells placed in a hypertonic environment
tend to shrink due to loss of water. In a
hypotonic environment, cells tend to swell
due to intake of water. The blood
maintains an isotonic environment so that
cells neither shrink nor swell. (credit:
Mariana Ruiz Villareal)
Need for Osmoregulation
The body does not exist in isolation. There is a constant input of water and
electrolytes into the system; osmoregulation is thus a constant process.
Biological systems constantly interact and exchange water and nutrients
with the environment by way of consumption of food and water and
through excretion in the form of sweat, urine, and feces. Without a
mechanism to regulate osmotic pressure, or when a disease damages this
mechanism, there is a tendency to accumulate toxic waste and either gain or
lose water, which can have dire consequences.
Mammalian systems have evolved to regulate not only the overall osmotic
pressure across membranes, but also specific concentrations of important
electrolytes in the three major fluid compartments: blood plasma,
extracellular fluid, and intracellular fluid. Since osmotic pressure is
regulated by the movement of water across membranes, the volume of the
fluid compartments can also change temporarily. Because blood plasma is
one of the fluid components, osmotic pressures have a direct bearing on
blood pressure.
Transport of Electrolytes across Plasmal Membranes
Electrolytes, such as sodium chloride, ionize in water, meaning that they
dissociate into their component ions. In water, sodium chloride (NaCl),
dissociates into the sodium ion (Na‘) and the chloride ion (CI-). The most
important ions, whose concentrations are very closely regulated in body
fluids, are the cations sodium (Na*), potassium (K*), calcium (Ca‘*?),
magnesium (Mg*?), and the anions chloride (CI’), carbonate (CO3°),
bicarbonate (HCO3)), and phosphate(PO3°). Electrolytes are lost from the
body during urination and perspiration. For this reason, athletes are
encouraged to replace electrolytes and fluids during periods of increased
activity and perspiration.
Osmotic pressure is influenced by the concentration of solutes in a solution.
It is directly proportional to the concentration of solute atoms or molecules,
and not dependent on the size of the solute molecules. Because some
compounds (known as electrolytes) dissociate into their component ions,
they add more solute particles into the solution and have a greater effect on
osmotic pressure, per mass than compounds that do not dissociate in water,
such as glucose.
Water can pass through membranes by passive diffusion. If electrolyte ions
could passively diffuse across membranes, it would be impossible to
maintain specific concentrations of ions in each fluid compartment
therefore they require special mechanisms to cross the semi-permeable
membranes in the body. This movement can be accomplished by facilitated
diffusion and active transport. Facilitated diffusion requires protein-based
channels for moving the solute. Active transport requires energy in the form
of ATP conversion, carrier proteins, or pumps in order to move ions against
the concentration gradient.
Osmoregulators and Osmoconformers
Persons lost at sea without any fresh water to drink are at risk of severe
dehydration because the human body cannot adapt to drinking seawater,
which is hypertonic in comparison to body fluids. Organisms such as
goldfish that can tolerate only a relatively narrow range of salinity are
referred to as stenohaline. About 90 percent of all bony fish are restricted to
either freshwater or seawater. They are incapable of osmotic regulation in
the opposite environment. It is possible, however, for a few fishes like
salmon to spend part of their life in fresh water and part in sea water.
Organisms like the salmon that can tolerate a relatively wide range of
salinity are referred to as euryhaline organisms. This is possible because
some fish have evolved osmoregulatory mechanisms to survive in all kinds
of aquatic environments. When they live in fresh water, their bodies tend to
take up water because the environment is relatively hypotonic, as illustrated
in [link]a. In such hypotonic environments, these fish do not drink much
water. Instead, they pass a lot of very dilute urine, and they achieve
electrolyte balance by active transport of salts through the gills. When they
move to a hypertonic marine environment, these fish start drinking sea
water; they excrete the excess salts through their gills and their urine, as
illustrated in [link]b. Most marine invertebrates, on the other hand, may be
isotonic with sea water; these are known as osmoconformers. Their body
fluid concentrations conform to changes in seawater concentration.
Cartilaginous fishes’ salt composition of the blood is similar to bony fishes;
however, the blood of sharks contains the organic compounds urea and
trimethylamine oxide (TMAO). This does not mean that their electrolyte
composition is similar to that of sea water. They achieve isotonicity with the
sea by storing large concentrations of urea. These animals that secrete urea
are called ureotelic animals. TMAO stabilizes proteins in the presence of
high urea levels, preventing the disruption of peptide bonds that would
occur in other animals exposed to similar levels of urea. Sharks have a
rectal gland which secretes salt and assists in osmoregulation.
Absorbs water through skin
Actively takes up ions
through gills
Drinks little
water
===> Movement of water
===> Movement of ions
Excretes dilute urine
(a) Osmoregulation in a freshwater environment
Loses water through skin
Drinks ample
water
Direction of ion Direction of water
movement movement
(Na*,K*,Ch)
Excretes ions through gills Excretes concentrated urine
(b) Osmoregulation in a saltwater environment
Fish are osmoregulators, but must use different mechanisms to
survive in (a) freshwater or (b) saltwater environments. (credit:
modification of work by Duane Raver, NOAA)
Kidneys and Osmoregulatory Organs
Although the kidneys are the major osmoregulatory organ, the skin and
lungs also play a role in the process. Water and electrolytes are lost through
sweat glands in the skin, which helps moisturize and cool the skin surface,
while the lungs expel a small amount of water in the form of mucous
secretions and via evaporation of water vapor.
Kidneys: The Main Osmoregulatory Organ
The kidneys, illustrated in [link], are a pair of bean-shaped structures that
are located just below and posterior to the liver in the peritoneal cavity. The
adrenal glands sit on top of each kidney. Kidneys filter blood and purify it.
All the blood in the human body is filtered many times a day by the
kidneys; these organs use up almost 25 percent of the oxygen absorbed
through the lungs to perform this function. The filtrate coming out of the
kidneys is called urine.
Renal artery
Adrenal
gland
Kidney Renal vein
Ureter
Renal
pelvis
Bladder
Urethra
Kidneys filter the blood,
producing urine that is stored in
the bladder prior to elimination
through the urethra. (credit:
modification of work by NCI)
Kidney Structure
Externally, the kidneys are surrounded by three layers, illustrated in [Link].
The outermost layer is a tough connective tissue layer called the renal
fascia. The second layer is called the perirenal fat capsule, which helps
anchor the kidneys in place. The third and innermost layer is the renal
capsule. Internally, the kidney has three regions—an outer cortex, a medulla
in the middle, and the renal pelvis in the region called the hilum of the
kidney. The hilum is the concave part of the bean-shape where blood
vessels and nerves enter and exit the kidney; it is also the point of exit for
the ureters. The renal cortex is granular due to the presence of nephrons—
the functional unit of the kidney. The medulla consists of multiple
pyramidal tissue masses, called the renal pyramids. In between the
pyramids are spaces called renal columns through which the blood vessels
pass. The tips of the pyramids, called renal papillae, point toward the renal
pelvis. There are, on average, eight renal pyramids in each kidney. The
renal pyramids along with the adjoining cortical region are called the lobes
of the kidney. The renal pelvis leads to the ureter on the outside of the
kidney. On the inside of the kidney, the renal pelvis branches out into two or
three extensions called the major calyces, which further branch into the
minor calyces. The ureters are urine-bearing tubes that exit the kidney and
empty into the urinary bladder.
Capillaries
Arteriole
Venule
; Renal pyramid
Renal vein
Renal artery
Renal pelvis
Medulla
Ureter
Renal fascia and cortex Cortex
The internal structure of the kidney is shown.
(credit: modification of work by NCI)
Because the kidney filters blood, its network of blood vessels is an
important component of its structure and function. The arteries, veins, and
nerves that supply the kidney enter and exit at the renal hilum. Renal blood
supply starts with the branching of the aorta into the renal arteries and ends
with the exiting of the renal veins to join the inferior vena cava.
As mentioned previously, the functional unit of the kidney is the nephron,
illustrated in [link]. Each kidney is made up of over one million nephrons
that dot the renal cortex, giving it a granular appearance when sectioned
sagittally. A nephron consists of three parts—a renal corpuscle, a renal
tubule, and the associated capillary network, which originates from the
arteries that supply blood to the kidney.
Proximal convoluted
Nephron tubule Peritubular
capillaries
Distal
convoluted
tubule
Efferent
arteriole
i=
/ Medulla
capsule
Afferent
arteriole
The nephron is the functional unit of the kidney. The
glomerulus and convoluted tubules are located in the
kidney cortex, while collecting ducts are located in the
pyramids of the medulla. (credit: modification of work by
NIDDK)
Renal Corpuscle
The renal corpuscle, located in the renal cortex, is made up of a network of
capillaries known as the glomerulus and the capsule, a cup-shaped chamber
that surrounds it, called the glomerular or Bowman's capsule.
Renal Tubule
The renal tubule is a long and convoluted structure that emerges from the
glomerulus and can be divided into three parts based on function. The first
part is called the proximal convoluted tubule (PCT) due to its proximity
to the glomerulus; it stays in the renal cortex. The second part is called the
loop of Henle, or nephritic loop, because it forms a loop (with descending
and ascending limbs) that goes through the renal medulla. The third part of
the renal tubule is called the distal convoluted tubule (DCT) and this part
is also restricted to the renal cortex. The DCT, which is the last part of the
nephron, connects and empties its contents into collecting ducts that line the
medullary pyramids. The collecting ducts amass contents from multiple
nephrons and fuse together as they enter the papillae of the renal medulla.
Capillary Network within the Nephron
The capillary network that originates from the renal arteries supplies the
nephron with blood that needs to be filtered. The branch that enters the
glomerulus is called the afferent arteriole. The branch that exits the
glomerulus is called the efferent arteriole. Within the glomerulus, the
network of capillaries is called the glomerular capillary bed. Once the
efferent arteriole exits the glomerulus, it forms the peritubular capillary
network, which surrounds and interacts with parts of the renal tubule.
Kidney Function and Physiology
Kidneys filter blood in a three-step process. First, the nephrons filter blood
that runs through the capillary network in the glomerulus. Almost all
solutes, except for proteins, are filtered out into the glomerulus by a process
called glomerular filtration. The high arterial pressure and the permeable
membranes of the glomerulus (see below) combine to accomplish this
filtration. Second, the filtrate is collected in the renal tubules. Most of the
solutes get reabsorbed in the PCT by a process called tubular
reabsorption. In the loop of Henle, the filtrate continues to exchange
solutes and water with the renal medulla and the peritubular capillary
network. Water is also reabsorbed during this step. Then, additional solutes
and wastes are secreted into the kidney tubules during tubular secretion,
which is, in essence, the opposite process to tubular reabsorption. The
collecting ducts collect filtrate coming from the nephrons and fuse in the
medullary papillae. From here, the papillae deliver the filtrate, now called
urine, into the minor calyces that eventually connect to the ureters through
the renal pelvis. This entire process is illustrated in [link].
2. Proximal convoluted tubule:
reabsorbs ions, water, and
nutrients; removes toxins
and adjusts filtrate pH
5. Distal tubule:
selectively secretes
and absorbs different
ions to maintain blood
pH and electrolyte
balance
1. Glomerulus:
filters small
solutes from
the blood
6. Collecting
duct:
reabsorbs
solutes and
water from
the filtrate
4. Ascending loop
of Henle:
reabsorbs Na* and
CF from the filtrate
into the interstitial
fluid
3. Descending
loop of Henle:
aquaporins
allow water
to pass from
) the filtrate
into the
interstitial fluid
Each part of the nephron performs
a different function in filtering
waste and maintaining
homeostatic balance. (1) The
glomerulus forces small solutes
out of the blood by pressure. (2)
The proximal convoluted tubule
reabsorbs ions, water, and
nutrients from the filtrate into the
interstitial fluid, and actively
transports toxins and drugs from
the interstitial fluid into the
filtrate. The proximal convoluted
tubule also adjusts blood pH by
selectively secreting ammonia
(NH3) into the filtrate, where it
reacts with H* to form NH,". The
more acidic the filtrate, the more
ammonia is secreted. (3) The
descending loop of Henle is lined
with cells containing aquaporins
that allow water to pass from the
filtrate into the interstitial fluid.
(4) In the thin part of the
ascending loop of Henle, Na* and
Cl ions diffuse into the interstitial
fluid. In the thick part, these same
ions are actively transported into
the interstitial fluid. Because salt
but not water is lost, the filtrate
becomes more dilute as it travels
up the limb. (5) In the distal
convoluted tubule, K* and H™ ions
are selectively secreted into the
filtrate, while Na’, Cl’, and HCO3"
ions are reabsorbed to maintain
pH and electrolyte balance in the
blood. (6) The collecting duct
reabsorbs solutes and water from
the filtrate, forming dilute urine.
(credit: modification of work by
NIDDK)
Glomerular Filtration
Glomerular filtration filters out most of the solutes due to high blood
pressure and specialized membranes in the afferent arteriole. The blood
pressure in the glomerulus is maintained independent of factors that affect
systemic blood pressure. The “leaky” connections between the endothelial
cells of the glomerular capillary network allow solutes to pass through
easily. All solutes in the glomerular capillaries, except for macromolecules
like proteins, pass through by passive diffusion. There is no energy
requirement at this stage of the filtration process; high arterial blood
pressure does the work at this stage.
Tubular Reabsorption and Secretion
Tubular reabsorption occurs in the PCT part of the renal tubule. Almost all
nutrients (e.g. glucose, amino acids) are reabsorbed, and this occurs either
by passive or active transport. Reabsorption of water and some key
electrolytes are regulated and can be influenced by hormones. Sodium
(Na‘) is the most abundant ion and most of it is reabsorbed by active
transport and then transported to the peritubular capillaries. Because Na’ is
actively transported out of the tubule, water follows it to even out the
osmotic pressure. Water is also independently reabsorbed into the
peritubular capillaries due to the presence of aquaporins, or water channels,
in the PCT. This occurs due to the low blood pressure and high osmotic
pressure in the peritubular capillaries. However, every solute has a transport
maximum and the excess is not reabsorbed.
In the loop of Henle, the permeability of the membrane changes. The
descending limb is permeable to water, not solutes; the opposite is true for
the ascending limb. Additionally, the loop of Henle invades the renal
medulla, which is naturally high in salt concentration and tends to absorb
water from the renal tubule and concentrate the filtrate. The osmotic
gradient increases as it moves deeper into the medulla. Because two sides of
the loop of Henle perform opposing functions, as illustrated in [link], it acts
as a countercurrent multiplier. The vasa recta around it acts as the
countercurrent exchanger.
Filtrate enters the Filtrate exits the
descending limb. ascending limb.
Interstitial
Loop of
fluid
Henle
The loop of Henle acts as a
countercurrent multiplier that
uses energy to create
concentration gradients. The
descending limb is water
permeable. Water flows from
the filtrate to the interstitial
fluid, so osmolality inside the
limb increases as it descends
into the renal medulla. At the
bottom, the osmolality is
higher inside the loop than in
the interstitial fluid. Thus, as
filtrate enters the ascending
limb, Na* and CI ions exit
through ion channels present
in the plasma membrane.
Further up, Na” is actively
transported out of the filtrate
and Cl follows. Osmolarity
is given in units of
milliosmoles per liter
(mOsm/L).
Hypertension (high blood pressure) is a common problem for humans, and
is usually treated with a variety of drugs that act on various processes
occurring in the kidney. One class of hypertension drugs is the so-called
"loop diuretics", which inhibit the reabsorption of Na* and CI ions by the
ascending limb of the loop of Henle. A side effect is that they increase
urination. Why do you think this is the case?
By the time the filtrate reaches the DCT, most of the urine and solutes have
been reabsorbed. If the body requires additional water, all of it can be
reabsorbed at this point. Further reabsorption is controlled by hormones,
which will be discussed in a later section. Excretion of wastes occurs due to
lack of reabsorption combined with tubular secretion. Undesirable products
like metabolic wastes, urea, uric acid, and certain drugs, are excreted by
tubular secretion. Most of the tubular secretion happens in the DCT, but
some occurs in the early part of the collecting duct. Kidneys also maintain
an acid-base balance by secreting excess H" ions.
Nitrogenous Waste
Of the four major macromolecules in biological systems, both proteins and
nucleic acids contain nitrogen. During the catabolism, or breakdown, of
nitrogen-containing macromolecules, carbon, hydrogen, and oxygen are
extracted and stored in the form of carbohydrates and fats. Excess nitrogen
is excreted from the body. Nitrogenous wastes tend to form toxic ammonia,
which raises the pH of body fluids. The formation of ammonia itself
requires energy in the form of ATP and large quantities of water to dilute it
out of a biological system. It is quite toxic even at relatively low
concentrations. Animals that live in aquatic environments tend to release
ammonia directly into the water in the urine; they have access to sufficient
water to dilute this waste product to non-toxic levels. Animals that excrete
ammonia are said to be ammonotelic. Terrestrial organisms have evolved
other mechanisms to process and excrete nitrogenous wastes. The animals
first detoxify ammonia by converting it into a relatively nontoxic form such
as urea or uric acid. Mammals, including humans, produce urea, whereas
reptiles and many terrestrial invertebrates produce uric acid. Animals that
secrete urea as the primary nitrogenous waste material are called ureotelic
animals.
Nitrogenous Waste in Terrestrial Animals: Urea
Urea formation is the primary mechanism by which mammals convert
ammonia to urea. Urea is made in the liver and excreted in urine. The
overall chemical reaction by which ammonia is converted to urea is 2 NH3
(ammonia) + CO, + 3 ATP + H»O —~ H»N-CO-NH)> (urea) + 2 ADP + 4 P;
+ AMP.
Note:
Evolution Connection
Excretion of Nitrogenous Waste
The theory of evolution proposes that life started in an aquatic
environment. It is not surprising to see that biochemical pathways like the
urea cycle evolved to adapt to a changing environment when terrestrial life
forms evolved. Arid conditions probably led to the evolution of the uric
acid pathway as a means of conserving water.
Nitrogenous Waste in Birds and Reptiles: Uric Acid
Birds, reptiles, and most terrestrial arthropods convert toxic ammonia to
uric acid or the closely related compound guanine (guano) instead of urea.
Mammals also form some uric acid during breakdown of nucleic acids. Uric
acid is a compound similar to purines found in nucleic acids. It is water
insoluble and tends to form a white paste or powder; it is excreted by birds,
insects, and reptiles. Conversion of ammonia to uric acid requires more
energy and is much more complex than conversion of ammonia to urea
[link], but the pay off is that uric acid requires much less water when
excreted.
a At NH,
Zz Ammonia
* a 5
Uric acid
LE.
(a) Many invertebrates and (b) Mammals, many adult (c) Insects, land snails, birds,
aquatic species excrete amphibians, and some marine and many reptiles excrete
ammonia. species excrete urea. uric acid.
Nitrogenous waste is excreted in different forms by different
species. These include (a) ammonia, (b) urea, and (c) uric acid.
(credit a: modification of work by Eric Engbretson, USFWS;
credit b: modification of work by B. "Moose" Peterson, USFWS;
credit c: David A. Rintoul)
Gout
In some animals, uric acid can build up under certain conditions, or as
consequence of a diet high in nitrogenous compounds (e.g. nucleotides). In
those situations, uric acid tends to crystallize and form kidney stones. Uric
acid buildup may also cause a painful condition called gout, where uric acid
crystals accumulate in the joints, as illustrated in [link]. Food choices that
reduce the amount of nitrogenous compounds in the diet help reduce the
risk of gout. For example, tea, coffee, and chocolate have purine-like
compounds, called xanthines, and should be avoided by people with gout
and kidney stones.
Gout causes the inflammation visible
in this person’s left big toe joint.
(credit: "Gonzosft"/Wikimedia
Commons)
Musculoskeletal System
Introduction
"Of all the constituents of the human body, bone is the hardest, the driest,
the earthiest and the coldest; and, excepting only the teeth, it is devoid of
sensation. God, the great Creator of all things, formed its substance to this
specification with good reason, intending it to be like a foundation for the
whole body; for it the fabric of the human body bones perform the same
function as do walls and beams in houses, poles in tents, and keels and ribs
in boats." Andreas Vesalius, Flemish anatomist, in De Humanis Corporis
Fabrica, 1543
As Vesalius recognized long ago, the muscular and skeletal systems provide
support to the body and allow for a wide range of movement. The bones of
the skeletal system protect the body’s internal organs and support the
weight of the body. The muscles of the muscular system contract and pull
on the bones, allowing for movements as diverse as standing, walking,
running, and grasping items. Injury or disease affecting the musculoskeletal
system can be very debilitating. In humans, the most common
musculoskeletal diseases worldwide are caused by malnutrition. Ailments
that affect the joints are also widespread, such as arthritis, which can make
movement difficult and—in advanced cases—completely impair mobility.
Types of Skeletal Systems
A skeletal system is necessary to support the body, protect internal organs,
and allow for the movement of an organism. There are three different
skeleton designs that fulfill these functions: hydrostatic skeleton,
exoskeleton, and endoskeleton.
Hydrostatic Skeleton
A hydrostatic skeleton is a skeleton formed by a fluid-filled compartment
within the body, called the coelom. The organs of the coelom are supported
by the aqueous fluid, which also resists external compression. This
compartment is under hydrostatic pressure because of the fluid and supports
the other organs of the organism. This type of skeletal system is found in
soft-bodied animals such as sea anemones, earthworms, Cnidaria, and other
invertebrates ([link]).
The skeleton of the red-knobbed
sea star (Protoreaster linckii) is an
example of a hydrostatic skeleton.
(credit: “Amada44”/Wikimedia
Commons)
Movement in a hydrostatic skeleton is provided by muscles that surround
the coelom. The muscles in a hydrostatic skeleton contract to change the
shape of the coelom; the pressure of the fluid in the coelom produces
movement. For example, earthworms move by waves of muscular
contractions of the skeletal muscle of the body wall hydrostatic skeleton,
called peristalsis, which alternately shorten and lengthen the body.
Lengthening the body extends the anterior end of the organism. Most
organisms have a mechanism to fix themselves in the substrate. Shortening
the muscles then draws the posterior portion of the body forward. Although
a hydrostatic skeleton is well-suited to invertebrate organisms such as
earthworms and some aquatic organisms, it is not an efficient skeleton for
terrestrial animals.
Exoskeleton
An exoskeleton is a chitinous external skeleton that consists of a hard
encasement on the surface of an organism. For example, the shells of crabs
and insects are exoskeletons ([link]). This skeleton type provides defense
against predators, supports the body, and allows for movement through the
contraction of attached muscles. As with endoskeletons (see below),
muscles must cross a joint inside the exoskeleton. Shortening of the muscle
thus changes the relationship of the two segments of the exoskeleton.
Arthropods such as crabs and lobsters have exoskeletons that consist of 30—
50 percent chitin, a polysaccharide derivative of glucose that is a strong but
flexible material. Chitin is secreted by the epidermal cells. The exoskeleton
is further strengthened by the addition of calcium carbonate in organisms
such as the lobster. Because the exoskeleton is acellular, arthropods must
periodically shed their exoskeletons as they grow, because the exoskeleton
does not grow as the organism grows.
Muscles attached to the
exoskeleton of the Halloween crab
(Gecarcinus quadratus) allow it to
move.
Endoskeleton
An endoskeleton is a skeleton that consists of hard, mineralized structures
located within the soft tissue of organisms. The bones of vertebrates are
composed of tissues and mineralized tissues. Endoskeletons provide support
for the body, protect internal organs, and allow for movement through
contraction of muscles attached to the skeleton.
The skeletons of humans and
horses are examples of
endoskeletons. (credit: Ross
Murphy)
As an example, the human skeleton is an endoskeleton that consists of 206
bones in the adult. It has five main functions: providing support to the body,
storing minerals and lipids, producing blood cells, protecting internal
organs, and allowing for movement. The skeletal system in vertebrates is
divided into the axial skeleton (which consists of the skull, vertebral
column, and rib cage), and the appendicular skeleton (which consists of the
shoulders, limb bones, the pectoral girdle, and the pelvic girdle).
Main divisions of the vertebrate skeleton
Ossicles
(inner ear)
Hyoid bone
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The axial skeleton of humans
consists of the bones of the skull,
ossicles of the middle ear, hyoid
bone, vertebral column, and rib
cage. (credit: modification of work
by Mariana Ruiz Villareal)
The human appendicular
skeleton is composed of the
bones of the pectoral limbs
(arm, forearm, hand), the pelvic
limbs (thigh, leg, foot), the
pectoral girdle, and the pelvic
girdle. (credit: modification of
work by Mariana Ruiz
Villareal)
Evolution of Body Design for Locomotion on Land
The transition of vertebrates from fish ancestors to land-dwelling animals
required a number of changes in body design, since movement on land
poses challenges that are different from those posed by movement in water.
Water provides a certain amount of lift, which is missing on land, so
muscles are needed to provide that lift on land. It also provides a medium to
push against, and many fish use lateral undulations to push against the
water and generate forward movement. Air does not provide the same
resistance, and so lateral undulations on land would not produce much
movement forward.
As certain fish began to move onto land, they retained their lateral
undulation form of locomotion. However, instead of pushing against water,
their fins became points of contact with the ground, and the lateral
undulations became rotations about those points of contact. The lack of
bouyancy provided by water led to increased ossification of the bones and
strengthening of the muscles, as well as providing selective pressure that
resulted in changes in arrangement of the "wrist" bones of these early
tetrapods. The effect of gravity also led to changes in the axial skeleton,
since rotations around the contact points with the ground caused new
torsional strains on the vertebral column. A firmer, more ossified vertebral
column became common in land animals, because it reduces the strain and
also provides strength to support the weight of the body. In later tetrapods
the vertebrae began allowing for vertical rather than lateral flexing. The
vertebrae of the neck also evolved to allow movement of the head
independently of the body, a range of motion not found in fish.
In early terrestrial tetrapods (({link]), the limbs were splayed out to the side,
reflecting the position of the fins in their fishy ancestors. This resulted in a
form of motion that was similar to performing push-ups while walking,
which requires large muscles to move the limbs toward the midline. This is
not an efficient form of locomotion, and selective pressures soon led to a
configuration where the limbs were placed undermeath the body, so that
each stride requires less energy to move the animal forward. The rotation
around the point of contact became a motion that is more like a pendulum
when the limbs are underneath the body, producing a stride that was much
more efficient for movement over land. Additional changes were required
in the appendicular skeleton to accommodate the new ranges of motion that
were enabled by that limb placement.
Muscles
Muscle cells are specialized for contraction. Muscles allow for motions
such as walking, and they also facilitate bodily processes such as respiration
and digestion. The body contains three types of muscle tissue: skeletal
muscle, cardiac muscle, and smooth muscle ((link]).
Skeletal muscle Smooth muscle Cardiac muscle
The body contains three types of muscle tissue: skeletal muscle,
smooth muscle, and cardiac muscle, visualized here using light
microscopy. Smooth muscle cells are short, tapered at each end,
and have only one plump nucleus in each. Cardiac muscle cells
are branched and striated, but short. The cytoplasm may branch,
and they have one nucleus in the center of the cell. (credit:
modification of work by NCI, NIH; scale-bar data from Matt
Russell)
Skeletal muscle tissue forms skeletal muscles, which attach to bones or
skin and control locomotion and any movement that can be consciously
controlled. Because it can be controlled by thought, skeletal muscle is also
called voluntary muscle. Skeletal muscles are long and cylindrical in
appearance; when viewed under a microscope, skeletal muscle tissue has a
striped or striated appearance. The striations are caused by the regular
arrangement of contractile proteins (actin and myosin). Actin is a globular
contractile protein that interacts with myosin for muscle contraction.
Skeletal muscle cells form by fusion of many muscle cells called myoblasts,
and thus have multiple nuclei present in a single cell.
Smooth muscle tissue occurs in the walls of hollow organs such as the
intestines, stomach, and urinary bladder, and around passages such as the
respiratory tract and blood vessels. Smooth muscle has no striations, is not
under voluntary control, has only one nucleus per cell, is tapered at both
ends, and is also called involuntary muscle.
Cardiac muscle tissue is only found in the heart, and cardiac contractions
pump blood throughout the body and maintain blood pressure. Like skeletal
muscle, cardiac muscle is striated, but unlike skeletal muscle, cardiac
muscle cannot be consciously controlled and is called involuntary muscle. It
has one nucleus per cell, is branched, and is distinguished by the presence
of intercalated disks. Intercalated disks are ion-permeable junctions
between individual cardiac muscle cells which allow for synchronized
contractions of the various regions of the heart.
Skeletal Muscle Fiber Structure
Each skeletal muscle fiber is a skeletal muscle cell. These cells are
incredibly large, with diameters of up to 100 jm and lengths of up to 30
cm. The plasma membrane of a skeletal muscle fiber is called the
sarcolemma. The sarcolemma is the site of action potential conduction,
which triggers muscle contraction. Within each muscle fiber are myofibrils
—long cylindrical structures that lie parallel to the muscle fiber. Myofibrils
run the entire length of the muscle fiber, and because they are only
approximately 1.2 am in diameter, hundreds to thousands can be found
inside one muscle fiber. They attach to the sarcolemma at their ends, so that
as myofibrils shorten, the entire muscle cell contracts ([Link]).
Sarcolemma
Sarcoplasm
Myofibrils
Striations
Muscle fiber
A skeletal muscle cell is surrounded by a plasma membrane called
the sarcolemma with a cytoplasm called the sarcoplasm. A muscle
fiber is composed of many fibrils, packaged into orderly units.
The striated appearance of skeletal muscle tissue is a result of repeating
bands of the proteins actin and myosin that are present along the length of
myofibrils. Dark A bands and light I bands repeat along myofibrils, and the
alignment of myofibrils in the cell causes the entire cell to appear striated or
banded.
Each I band has a dense line running vertically through the middle called a
Z disc or Z line. The Z discs mark the border of units called sarcomeres,
which are the functional units of skeletal muscle. One sarcomere is the
space between two consecutive Z discs and contains one entire A band and
two halves of an I band, one on either side of the A band. A myofibril is
composed of many sarcomeres running along its length, and as the
sarcomeres individually contract, the myofibrils and muscle cells shorten
({link]).
Z line Sarcomere
Thin filament Thick filament
Myofibril
A sarcomere is the region from
one Z line to the next Z line. Many
sarcomeres are present in a
myofibril, resulting in the striation
pattern characteristic of skeletal
muscle.
Myofibrils are composed of smaller structures called myofilaments. There
are two main types of filaments: thick filaments and thin filaments; each
has different compositions and locations. Thick filaments occur only in the
A band of a myofibril. Thin filaments attach to a protein in the Z disc
called alpha-actinin and occur across the entire length of the I band and
partway into the A band. The region at which thick and thin filaments
overlap has a dense appearance, as there is little space between the
filaments. Thin filaments do not extend all the way into the A bands,
leaving a central region of the A band that only contains thick filaments.
This central region of the A band looks slightly lighter than the rest of the A
band and is called the H zone. The middle of the H zone has a vertical line
called the M line, at which accessory proteins hold together thick filaments.
Both the Z disc and the M line hold myofilaments in place to maintain the
structural arrangement and layering of the myofibril. Myofibrils are
connected to each other by intermediate, or desmin, filaments that attach to
the Z disc.
Thick and thin filaments are themselves composed of proteins. Thick
filaments are primarily composed of the protein myosin. The tail of a
myosin molecule connects with other myosin molecules to form the central
region of a thick filament near the M line, whereas the heads align on either
side of the thick filament where the thin filaments overlap. The primary
component of thin filaments is the actin protein. Two other components of
the thin filament are tropomyosin and troponin. Actin has binding sites for
myosin attachment. Strands of tropomyosin block the binding sites and
prevent actin—myosin interactions when the muscles are at rest. Troponin
consists of three globular subunits. One subunit binds to tropomyosin, one
subunit binds to actin, and one subunit binds Ca2* ions.
Sliding Filament Model of Contraction
For a muscle cell to contract, the sarcomere must shorten. However,
individual thick and thin filaments—the components of sarcomeres—do not
shorten. Instead, they slide by one another, causing the sarcomere to shorten
while the filaments remain the same length. The sliding filament theory of
muscle contraction was developed to explain the differences observed in the
lengths of the named bands on the sarcomere at different degrees of muscle
contraction and relaxation. The mechanism of contraction is the binding of
myosin to actin, forming cross-bridges that generate filament movement
([link]).
(a) Thin filament Thick filaments
(actin) (myosin)
Z line M line Z line
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When (a) a sarcomere (b) contracts, the Z lines move closer
together and the I band gets smaller. The A band stays the same
width and, at full contraction, the thin filaments overlap.
When a sarcomere shortens, some regions shorten whereas others stay the
same length. A sarcomere is defined as the distance between two
consecutive Z discs or Z lines; when a muscle contracts, the distance
between the Z discs is reduced. The H zone—the central region of the A
zone—contains only thick filaments and is shortened during contraction.
The I band contains only thin filaments and also shortens. The A band does
not shorten—it remains the same length—but A bands of different
sarcomeres move closer together during contraction, eventually
disappearing. Thin filaments are pulled by the thick filaments toward the
center of the sarcomere until the Z discs approach the thick filaments. The
zone of overlap, in which thin filaments and thick filaments occupy the
same area, increases as the thin filaments move inward.
ATP and Muscle Contraction
The motion of muscle shortening occurs as myosin heads bind to actin and
pull the actin inwards. This action requires energy, which is provided by
ATP. Myosin binds to actin at a binding site on the globular actin protein.
Myosin has another binding site for ATP, and acts as an enzyme to convert
ATP to ADP, releasing an inorganic phosphate molecule and energy. The
energy can be harnessed to promote contraction via the sliding filament
mechanism described above.
ATP binding causes myosin to release actin, allowing actin and myosin to
detach from each other. After this happens, the newly bound ATP is
converted to ADP and inorganic phosphate, P;. The enzyme at the binding
site on myosin is called ATPase. The energy released during ATP hydrolysis
changes the angle of the myosin head into a “cocked” position. The myosin
head is then in a position for further movement, possessing potential energy,
but ADP and P; are still attached. If actin binding sites are covered and
unavailable, the myosin will remain in the high energy configuration with
ATP hydrolyzed, but still attached.
If the actin binding sites are uncovered, a cross-bridge will form; that is, the
myosin head spans the distance between the actin and myosin molecules. P;
is then released, allowing myosin to expend the stored energy as a
conformational change. The myosin head moves toward the M line, pulling
the actin along with it. As the actin is pulled, the filaments move
approximately 10 nm toward the M line. This movement is called the power
stroke, as it is the step at which force is produced. As the actin is pulled
toward the M line, the sarcomere shortens and the muscle contracts.
When the myosin head is “cocked,” it contains energy and is in a high-
energy configuration. This energy is expended as the myosin head moves
through the power stroke; at the end of the power stroke, the myosin head is
in a low-energy position. After the power stroke, ADP is released; however,
the cross-bridge formed is still in place, and actin and myosin are bound
together. ATP can then attach to myosin, which allows the cross-bridge
cycle to start again and further muscle contraction can occur ([link]).
Tropomyosin
Ca2+
The active site on actin is
exposed as Ca?* binds or
troponin. Active site
Myosin head A Actin
@ The myosin head forms
a cross-bridge with actin.
During the power stroke,
® the myosin head bends,
and ADP and phosphate
are released.
Anew molecule of ATP
0) attaches to the myosin
head, causing the
cross-bridge to detach.
ATP hydrolyzes to ADP
6) and phosphate, which
returns the myosin to the
“cocked” position.
The cross-bridge muscle
contraction cycle, which is
triggered by Ca** binding to the
actin active site, is shown. With
each contraction cycle, actin
moves relative to myosin, and the
thick and thin filaments slide past
each other.
Regulatory Proteins
When a muscle is in a resting state, actin and myosin are separated. To keep
actin from binding to the active site on myosin, regulatory proteins block
the molecular binding sites. Tropomyosin blocks myosin binding sites on
actin molecules, preventing cross-bridge formation and preventing
contraction in a muscle without nervous input. Troponin binds to
tropomyosin and helps to position it on the actin molecule; it also binds
calcium ions.
To enable a muscle contraction, tropomyosin must change conformation,
uncovering the myosin-binding site on an actin molecule and allowing
cross-bridge formation. This can only happen in the presence of calcium,
which is kept at extremely low concentrations in the sarcoplasm. If present,
calcium ions bind to troponin, causing conformational changes in troponin
that allow tropomyosin to move away from the myosin binding sites on
actin. Once the tropomyosin is removed, a cross-bridge can form between
actin and myosin, triggering contraction. Cross-bridge cycling continues
until Ca** ions and ATP are no longer available and tropomyosin again
covers the binding sites on actin.
Excitation—Contraction Coupling
Excitation—contraction coupling is the link (transduction) between the
action potential generated in the sarcolemma and the start of a muscle
contraction. The trigger for calcium release from the sarcoplasmic
reticulum into the sarcoplasm is a neural signal. Each skeletal muscle fiber
is controlled by a motor neuron, which conducts signals from the brain or
spinal cord to the muscle. The area of the sarcolemma on the muscle fiber
that interacts with the neuron is called the motor end plate. The end of the
neuron’s axon is called the synaptic terminal, and it does not actually
contact the motor end plate. A small space called the synaptic cleft
separates the synaptic terminal from the motor end plate. Electrical signals
travel along the neuron’s axon, which branches through the muscle and
connects to individual muscle fibers at a neuromuscular junction. This
junction is functionally similar to a synapse between two nerve cells,
allowing a signal from the nerve cell to initiate an action potential in the
muscle plasma membrane. The action potential in the muscle cell causes
Ca** to be released from intracellular stores; this elevated calcium
concentration triggers the binding of actin and myosin, ATP hyrolysis, and
all of the other steps in contraction that are outlined above.
The neurotransmitter released at the neuromuscular junction in most
animals is acetylcholine. It is released from the nerve call ending and binds
to receptors on the muscle cell plasma membrane ((link]); these receptors
act as sodium channels when acetylcholine is bound to them. The influx of
sodium depolarizes the muscle cell, triggering an action potential in a
similar fashion to the action potential found in nerve cells. The
acetylcholine is rapidly degraded in the neuromuscular junction by an
enzyme called acetylcholinesterase. Various natural toxins (such as the
curare used on poison arrows by South American indigenous tribes) and
synthetic toxins (including nerve gases and insecticides) target the
components of the neuromuscular junction, including both the receptor and
the acetylcholinesterase. The deadly nerve gas known as Sarin irreversibly
inhibits acetylcholinesterase. What effect would Sarin have on muscle
contraction, and how does that effect lead to death?
(a)
Axon terminal
Synaptic vesicles
; Sarcolemma
Acetylcholine (muscle cell
receptor plasma
Synaptic cleft membrane)
Acetylcholine Acetylcholine
Acetylcholinesterase
Sarcoplasmic
reticulum
(muscle cell
endoplasmic
reticulum)
1. Acetylcholine released from the axon 5. Acetylcholinesterase removes acetylcholine
terminal binds to receptors on the from the synaptic cleft.
sarcolemma. 6. Ca?* is transported back into the
2. An action potential is generated and travels sarcoplasmic reticulum.
down the T tubule. 7. Tropomyosin binds active sites on actin
3. Ca?* is released from the sarcoplasmic causing the cross-bridge to detach.
reticulum in response to the change in
voltage.
4. Ca?* binds troponin; Cross-bridges form
between actin and myosin.
Acetylcholine effects at the neuromuscular
junction. The depolarization of the muscle plasma
membrane releases calcium from the sarcoplasmic
reticulum and initiates contraction of the muscle.